; 2014-09-03.182941
peak-motifs  -v 1 -title CEBPa_ChIP-seq_in_dog_liver_test_parameters -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifspeak_seq -max_seq_len 400 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db jaspar_core_vertebrates tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -motif_db Schmidt_CEBPa_motif tf $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -scan_markov 1 -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M



; 2014-09-03.182941
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/images_html


; 2014-09-03.182941
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifspeak_seq -from fasta -to fasta -mask non-dna| $RSAT/perl-scripts/sub-sequence -origin center -from -200 -to 199 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta


; 2014-09-03.182943
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -ml 30 -mis 0 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta


; 2014-09-03.182952
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2014-09-03.182954
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -legend -format png -title 'Sequence lengths; CEBPa_ChIP-seq_in_dog_liver_test_parameters' -ysize 200 -ycol 4 -yleg1 'Number of peaks' -xsize 800 -xcol 3 -xleg1 'Peak length' -xmin 0 -ymin 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2014-09-03.182955
$RSAT/perl-scripts/convert-features -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifspeak_seq -from galaxy_seq -to bed  | sed '1s/^.*/track name="test_peaks" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters test: peaks" visibility=2 use_score=1 color=13,115,67/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed


; 2014-09-03.183004
time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -l 1 -1str > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab_time.txt


; 2014-09-03.183004
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1  -out_format png -col_width 50 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2014-09-03.183005
time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -l 2 -1str > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab_time.txt


; 2014-09-03.183005
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1  -out_format png -col_width 50 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2014-09-03.183006
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'CEBPa_ChIP-seq_in_dog_liver_test_parameters' -origin center -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt


; 2014-09-03.183215
grep -v ";" $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles : ; test sequence; CEBPa_ChIP-seq_in_dog_liver_test_parameters' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300  -ymin 0 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2014-09-03.183216
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'CEBPa_ChIP-seq_in_dog_liver_test_parameters' -origin center -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt


; 2014-09-03.183448
grep -v ";" $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles : ; test sequence; CEBPa_ChIP-seq_in_dog_liver_test_parameters' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300  -ymin 0 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2014-09-03.183449
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -markov 4 -pseudo 0.01 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab_time.txt


; 2014-09-03.183500
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_6nt_mkv4 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_time.txt


; 2014-09-03.183559
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -markov 5 -pseudo 0.01 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab_time.txt


; 2014-09-03.183613
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_7nt_mkv5 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm_time.txt


; 2014-09-03.183705
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 8 -markov 6 -pseudo 0.01 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6.tab_time.txt


; 2014-09-03.183728
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_8nt_mkv6 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6_pssm_time.txt


; 2014-09-03.183825
time ($RSAT/perl-scripts/dyad-analysis -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -quick -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,ratio,zscore,rank -2str -noov -seqtype dna -l 3 -sp 0-20  -bg monads -pseudo 0.01 | perl -pe 's/n\{0\}//g' >$RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt


; 2014-09-03.184003
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 0 -prefix dyads -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_time.txt


; 2014-09-03.184110
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort  -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 6 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'CEBPa_ChIP-seq_in_dog_liver_test_parameters' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab_time.txt


; 2014-09-03.184446
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_6nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_time.txt


; 2014-09-03.184549
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort  -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 7 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'CEBPa_ChIP-seq_in_dog_liver_test_parameters' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab_time.txt


; 2014-09-03.184940
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_7nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_time.txt


; 2014-09-03.185039
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta -format fasta -sort  -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 8 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'CEBPa_ChIP-seq_in_dog_liver_test_parameters' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab_time.txt


; 2014-09-03.185504
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -pl $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_8nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_time.txt


; 2014-09-03.185607
time ($RSAT/perl-scripts/compare-scores -v 1  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -sc1 8 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/ -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -sc2 9 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/ -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab -sc3 8 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/ -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -sc4 9 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/ -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6.tab -sc5 8 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/ -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab -sc6 9 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/ -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -sc7 8 -suppress $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/ -ic 1 -lc -null . -suppress peak-motifs_ -suppress '.tab' | $RSAT/perl-scripts/row-stats -after 1 -sort  -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/merged_words/peak-motifs_merged_words.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/merged_words/peak-motifs_merged_words.tab_time.txt


; 2014-09-03.185607
$RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/merged_words/peak-motifs_merged_words.html


; 2014-09-03.185607
$RSAT/perl-scripts/draw-heatmap -min 0 -max 10  -out_format png -col_width 40 -rownames -gradient fire -row_height 16 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/merged_words/peak-motifs_merged_words_heatmap.png


; 2014-09-03.185608
rm -f $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/oligos_8nt_mkv6/peak-motifs_oligos-2str-noov_8nt_mkv6_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2014-09-03.185608
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tab


; 2014-09-03.185608
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tab


; 2014-09-03.185609
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tab


; 2014-09-03.185609
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tab


; 2014-09-03.185609
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tab


; 2014-09-03.185610
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tab


; 2014-09-03.185610
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tab


; 2014-09-03.185610
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tab


; 2014-09-03.185611
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tab


; 2014-09-03.185611
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tab


; 2014-09-03.185611
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tab


; 2014-09-03.185612
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tab


; 2014-09-03.185612
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tab


; 2014-09-03.185612
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tab


; 2014-09-03.185613
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tab


; 2014-09-03.185613
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tab


; 2014-09-03.185613
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tab


; 2014-09-03.185614
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tab


; 2014-09-03.185614
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tab


; 2014-09-03.185614
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tab


; 2014-09-03.185615
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1.tab


; 2014-09-03.185615
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.tab


; 2014-09-03.185615
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.tab


; 2014-09-03.185616
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.tab


; 2014-09-03.185616
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5.tab


; 2014-09-03.185616
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1.tab


; 2014-09-03.185617
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tab


; 2014-09-03.185617
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tab


; 2014-09-03.185617
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tab


; 2014-09-03.185618
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tab


; 2014-09-03.185618
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab


; 2014-09-03.185618
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab


; 2014-09-03.185619
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tab


; 2014-09-03.185619
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tab


; 2014-09-03.185619
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tab


; 2014-09-03.185620
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2014-09-03.185701
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2014-09-03.185703
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.185714
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.185717
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.185720
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.185725
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.185735
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.185746
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.185750
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.185755
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.185806
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.185810
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.185821
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.185824
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.185835
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.185838
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.185848
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.185858
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.185909
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.185920
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.185930
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.185941
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.185952
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.190003
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.190013
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.190023
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.190033
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.190043
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.190055
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.190105
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.190116
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.190127
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_jaspar_core_vertebrates


; 2014-09-03.190131
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_jaspar_core_vertebrates


; 2014-09-03.190135
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_jaspar_core_vertebrates


; 2014-09-03.190140
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_jaspar_core_vertebrates


; 2014-09-03.190144
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_jaspar_core_vertebrates


; 2014-09-03.190147
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab_time.txt


; 2014-09-03.190552
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.gml


; 2014-09-03.190556
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190557
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190558
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190559
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190600
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190601
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190602
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190603
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190604
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190605
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190606
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190607
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190608
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190609
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190610
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190611
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190612
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190613
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190615
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190616
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190617
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190618
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190619
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190620
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190622
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190623
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190624
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190625
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190626
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190627
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190628
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190629
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190630
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190632
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190632
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_Schmidt_CEBPa_motif


; 2014-09-03.190633
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_Schmidt_CEBPa_motif.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_Schmidt_CEBPa_motif.tab_time.txt


; 2014-09-03.190645
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_Schmidt_CEBPa_motif.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_Schmidt_CEBPa_motif.gml


; 2014-09-03.190646
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab_time.txt


; 2014-09-03.190658
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_6nt_mkv4_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed


; 2014-09-03.190701
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab


; 2014-09-03.190701
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.png


; 2014-09-03.190701
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab


; 2014-09-03.190702
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.png


; 2014-09-03.190702
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.190721
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv1_enrichment.png


; 2014-09-03.190721
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab_time.txt


; 2014-09-03.190730
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_6nt_mkv4_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed


; 2014-09-03.190732
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab


; 2014-09-03.190733
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.png


; 2014-09-03.190733
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab


; 2014-09-03.190733
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.png


; 2014-09-03.190734
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.190746
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv1_enrichment.png


; 2014-09-03.190746
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab_time.txt


; 2014-09-03.190756
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_6nt_mkv4_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_genomic.bed


; 2014-09-03.190758
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.tab


; 2014-09-03.190758
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.png


; 2014-09-03.190759
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.tab


; 2014-09-03.190759
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.png


; 2014-09-03.190759
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.190810
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv1_enrichment.png


; 2014-09-03.190810
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab_time.txt


; 2014-09-03.190821
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_6nt_mkv4_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_genomic.bed


; 2014-09-03.190822
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_site_distrib.tab


; 2014-09-03.190823
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_site_distrib.png


; 2014-09-03.190823
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_per_peak.tab


; 2014-09-03.190823
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_per_peak.png


; 2014-09-03.190824
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.190839
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_scan_mkv1_enrichment.png


; 2014-09-03.190839
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab_time.txt


; 2014-09-03.190851
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_6nt_mkv4_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_genomic.bed


; 2014-09-03.190853
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_site_distrib.tab


; 2014-09-03.190854
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_site_distrib.png


; 2014-09-03.190854
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_per_peak.tab


; 2014-09-03.190854
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_per_peak.png


; 2014-09-03.190855
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.190913
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_scan_mkv1_enrichment.png


; 2014-09-03.190913
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab_time.txt


; 2014-09-03.190925
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_6nt_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_6nt_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed


; 2014-09-03.190927
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab


; 2014-09-03.190927
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.png


; 2014-09-03.190927
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab


; 2014-09-03.190928
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.png


; 2014-09-03.190928
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.190947
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.png


; 2014-09-03.190947
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab_time.txt


; 2014-09-03.190959
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_6nt_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_6nt_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed


; 2014-09-03.191000
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab


; 2014-09-03.191001
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.png


; 2014-09-03.191001
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab


; 2014-09-03.191002
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.png


; 2014-09-03.191002
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191021
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.png


; 2014-09-03.191022
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab_time.txt


; 2014-09-03.191032
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_6nt_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_6nt_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed


; 2014-09-03.191033
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab


; 2014-09-03.191033
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.png


; 2014-09-03.191034
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab


; 2014-09-03.191034
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.png


; 2014-09-03.191034
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191048
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.png


; 2014-09-03.191048
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab_time.txt


; 2014-09-03.191101
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_6nt_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_6nt_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_genomic.bed


; 2014-09-03.191102
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.tab


; 2014-09-03.191102
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.png


; 2014-09-03.191103
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.tab


; 2014-09-03.191103
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.png


; 2014-09-03.191103
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191121
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.png


; 2014-09-03.191121
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab_time.txt


; 2014-09-03.191137
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_6nt_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_6nt_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_genomic.bed


; 2014-09-03.191138
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.tab


; 2014-09-03.191138
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.png


; 2014-09-03.191139
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.tab


; 2014-09-03.191139
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.png


; 2014-09-03.191139
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191203
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.png


; 2014-09-03.191204
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab_time.txt


; 2014-09-03.191215
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_7nt_mkv5_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed


; 2014-09-03.191217
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.tab


; 2014-09-03.191217
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.png


; 2014-09-03.191218
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.tab


; 2014-09-03.191218
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.png


; 2014-09-03.191219
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191235
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv1_enrichment.png


; 2014-09-03.191235
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab_time.txt


; 2014-09-03.191246
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_7nt_mkv5_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed


; 2014-09-03.191247
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.tab


; 2014-09-03.191248
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.png


; 2014-09-03.191248
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.tab


; 2014-09-03.191248
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.png


; 2014-09-03.191248
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191301
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv1_enrichment.png


; 2014-09-03.191301
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab_time.txt


; 2014-09-03.191311
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_7nt_mkv5_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed


; 2014-09-03.191313
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.tab


; 2014-09-03.191313
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.png


; 2014-09-03.191313
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.tab


; 2014-09-03.191314
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.png


; 2014-09-03.191314
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191327
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv1_enrichment.png


; 2014-09-03.191328
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab_time.txt


; 2014-09-03.191338
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_7nt_mkv5_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_genomic.bed


; 2014-09-03.191339
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_site_distrib.tab


; 2014-09-03.191339
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_site_distrib.png


; 2014-09-03.191339
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_per_peak.tab


; 2014-09-03.191340
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_per_peak.png


; 2014-09-03.191340
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191353
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_scan_mkv1_enrichment.png


; 2014-09-03.191353
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab_time.txt


; 2014-09-03.191404
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_7nt_mkv5_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_genomic.bed


; 2014-09-03.191405
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_site_distrib.tab


; 2014-09-03.191405
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_site_distrib.png


; 2014-09-03.191405
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_per_peak.tab


; 2014-09-03.191406
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_per_peak.png


; 2014-09-03.191406
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191419
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_scan_mkv1_enrichment.png


; 2014-09-03.191419
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab_time.txt


; 2014-09-03.191431
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_7nt_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_7nt_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed


; 2014-09-03.191433
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab


; 2014-09-03.191433
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.png


; 2014-09-03.191434
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab


; 2014-09-03.191434
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.png


; 2014-09-03.191434
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191453
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.png


; 2014-09-03.191454
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab_time.txt


; 2014-09-03.191506
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_7nt_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_7nt_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed


; 2014-09-03.191508
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab


; 2014-09-03.191508
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.png


; 2014-09-03.191508
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab


; 2014-09-03.191509
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.png


; 2014-09-03.191509
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191527
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.png


; 2014-09-03.191527
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab_time.txt


; 2014-09-03.191539
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_7nt_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_7nt_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed


; 2014-09-03.191541
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab


; 2014-09-03.191541
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.png


; 2014-09-03.191541
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab


; 2014-09-03.191542
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.png


; 2014-09-03.191542
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191600
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.png


; 2014-09-03.191601
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab_time.txt


; 2014-09-03.191613
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_7nt_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_7nt_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_genomic.bed


; 2014-09-03.191615
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab


; 2014-09-03.191615
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.png


; 2014-09-03.191615
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab


; 2014-09-03.191616
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.png


; 2014-09-03.191616
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191633
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.png


; 2014-09-03.191634
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab_time.txt


; 2014-09-03.191646
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_7nt_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_7nt_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_genomic.bed


; 2014-09-03.191648
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.tab


; 2014-09-03.191648
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.png


; 2014-09-03.191648
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.tab


; 2014-09-03.191649
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.png


; 2014-09-03.191649
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191707
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.png


; 2014-09-03.191707
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab_time.txt


; 2014-09-03.191719
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_8nt_mkv6_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_8nt_mkv6_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites_genomic.bed


; 2014-09-03.191722
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_site_distrib.tab


; 2014-09-03.191722
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_8nt_mkv6_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_site_distrib.png


; 2014-09-03.191722
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites_per_peak.tab


; 2014-09-03.191723
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_8nt_mkv6_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites_per_peak.png


; 2014-09-03.191723
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191741
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_scan_mkv1_enrichment.png


; 2014-09-03.191741
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab_time.txt


; 2014-09-03.191752
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_8nt_mkv6_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_8nt_mkv6_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites_genomic.bed


; 2014-09-03.191755
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_site_distrib.tab


; 2014-09-03.191755
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_8nt_mkv6_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_site_distrib.png


; 2014-09-03.191755
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites_per_peak.tab


; 2014-09-03.191756
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_8nt_mkv6_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites_per_peak.png


; 2014-09-03.191756
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191816
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_scan_mkv1_enrichment.png


; 2014-09-03.191816
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab_time.txt


; 2014-09-03.191828
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_8nt_mkv6_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_8nt_mkv6_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites_genomic.bed


; 2014-09-03.191830
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_site_distrib.tab


; 2014-09-03.191830
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_8nt_mkv6_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_site_distrib.png


; 2014-09-03.191831
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites_per_peak.tab


; 2014-09-03.191831
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_8nt_mkv6_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites_per_peak.png


; 2014-09-03.191832
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191851
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_scan_mkv1_enrichment.png


; 2014-09-03.191852
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab_time.txt


; 2014-09-03.191902
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_8nt_mkv6_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_8nt_mkv6_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites_genomic.bed


; 2014-09-03.191904
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_site_distrib.tab


; 2014-09-03.191904
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_8nt_mkv6_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_site_distrib.png


; 2014-09-03.191905
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites_per_peak.tab


; 2014-09-03.191905
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_8nt_mkv6_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites_per_peak.png


; 2014-09-03.191905
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191921
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_scan_mkv1_enrichment.png


; 2014-09-03.191922
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab_time.txt


; 2014-09-03.191932
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="oligos_8nt_mkv6_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: oligos_8nt_mkv6_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites_genomic.bed


; 2014-09-03.191933
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_site_distrib.tab


; 2014-09-03.191934
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_8nt_mkv6_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_site_distrib.png


; 2014-09-03.191934
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites_per_peak.tab


; 2014-09-03.191934
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_8nt_mkv6_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites_per_peak.png


; 2014-09-03.191935
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.191948
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_scan_mkv1_enrichment.png


; 2014-09-03.191948
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab_time.txt


; 2014-09-03.192000
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_8nt_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_8nt_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites_genomic.bed


; 2014-09-03.192002
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_site_distrib.tab


; 2014-09-03.192002
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_8nt_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_site_distrib.png


; 2014-09-03.192002
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites_per_peak.tab


; 2014-09-03.192003
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_8nt_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites_per_peak.png


; 2014-09-03.192003
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192022
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_scan_mkv1_enrichment.png


; 2014-09-03.192023
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab_time.txt


; 2014-09-03.192035
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_8nt_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_8nt_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites_genomic.bed


; 2014-09-03.192036
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_site_distrib.tab


; 2014-09-03.192037
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_8nt_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_site_distrib.png


; 2014-09-03.192037
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites_per_peak.tab


; 2014-09-03.192037
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_8nt_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites_per_peak.png


; 2014-09-03.192038
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192056
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_scan_mkv1_enrichment.png


; 2014-09-03.192056
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab_time.txt


; 2014-09-03.192107
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_8nt_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_8nt_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_genomic.bed


; 2014-09-03.192109
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_site_distrib.tab


; 2014-09-03.192109
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_8nt_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_site_distrib.png


; 2014-09-03.192109
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_per_peak.tab


; 2014-09-03.192110
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_8nt_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_per_peak.png


; 2014-09-03.192110
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192127
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_scan_mkv1_enrichment.png


; 2014-09-03.192127
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab_time.txt


; 2014-09-03.192140
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_8nt_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_8nt_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_genomic.bed


; 2014-09-03.192141
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_site_distrib.tab


; 2014-09-03.192141
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_8nt_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_site_distrib.png


; 2014-09-03.192141
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_per_peak.tab


; 2014-09-03.192142
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_8nt_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_per_peak.png


; 2014-09-03.192142
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192159
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_scan_mkv1_enrichment.png


; 2014-09-03.192159
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab_time.txt


; 2014-09-03.192212
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="positions_8nt_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: positions_8nt_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_genomic.bed


; 2014-09-03.192213
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_site_distrib.tab


; 2014-09-03.192213
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_8nt_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_site_distrib.png


; 2014-09-03.192214
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_per_peak.tab


; 2014-09-03.192214
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_8nt_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_per_peak.png


; 2014-09-03.192214
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192232
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_scan_mkv1_enrichment.png


; 2014-09-03.192233
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab_time.txt


; 2014-09-03.192245
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="dyads_m1" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: dyads_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_genomic.bed


; 2014-09-03.192247
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab


; 2014-09-03.192247
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png


; 2014-09-03.192248
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab


; 2014-09-03.192248
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m1' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png


; 2014-09-03.192248
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192305
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.png


; 2014-09-03.192305
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab_time.txt


; 2014-09-03.192318
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="dyads_m2" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: dyads_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_genomic.bed


; 2014-09-03.192319
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab


; 2014-09-03.192319
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png


; 2014-09-03.192319
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab


; 2014-09-03.192320
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m2' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png


; 2014-09-03.192320
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192338
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.png


; 2014-09-03.192338
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab_time.txt


; 2014-09-03.192348
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="dyads_m3" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: dyads_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_genomic.bed


; 2014-09-03.192350
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab


; 2014-09-03.192350
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.png


; 2014-09-03.192351
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab


; 2014-09-03.192351
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m3' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.png


; 2014-09-03.192351
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192403
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.png


; 2014-09-03.192404
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab_time.txt


; 2014-09-03.192416
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="dyads_m4" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: dyads_m4" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_genomic.bed


; 2014-09-03.192417
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.tab


; 2014-09-03.192417
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.png


; 2014-09-03.192418
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.tab


; 2014-09-03.192418
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m4' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.png


; 2014-09-03.192418
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192438
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_scan_mkv1_enrichment.png


; 2014-09-03.192438
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab_time.txt


; 2014-09-03.192448
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab -coord $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed -origin center -to bed  | sed '1s/^.*/track name="dyads_m5" description="RSAT peak-motifs CEBPa_ChIP-seq_in_dog_liver_test_parameters: dyads_m5" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_genomic.bed


; 2014-09-03.192450
grep -v '^;' $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.tab


; 2014-09-03.192450
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.png


; 2014-09-03.192450
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.tab


; 2014-09-03.192451
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m5' -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.png


; 2014-09-03.192451
time ($RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_scan_mkv1_enrichment.tab) >& $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_scan_mkv1_enrichment.tab_time.txt


; 2014-09-03.192502
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_scan_mkv1_enrichment.png


; 2014-09-03.192503
cat $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab 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$RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2014-09-03.192503
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$RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/peak-motifs_oligos_8nt_mkv6_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/peak-motifs_positions_8nt_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_genomic.bed $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_genomic.bed > $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/sites/peak-motifs_all_motifs_seqcoord.bed


; 2014-09-03.192526
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title CEBPa_ChIP-seq_in_dog_liver_test_parameters -i $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifspeak_seq -max_seq_len 400 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db jaspar_core_vertebrates tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -motif_db Schmidt_CEBPa_motif tf $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf -scan_markov 1 -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	30
;	purge_mismatches      	0
;	origin                	center
;	profiles_ci           	20
;	profiles_max_graphs   	20
;	profiles_strand       	-1str
;	composition_oligo_lengths	1,2
;	profiles_noov         	-ovlp
;	strand                	-2str
;	disco_noov            	-noov
;	oligo_min_len         	6
;	oligo_max_len         	8
;	patterns_max_rank     	100
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	-2
;	oligo_max_mkv         	-2
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	5
; Input files
;	motif_db_Schmidt_CEBPa_motif	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.tf
;	motif_db_jaspar_core_vertebrates	/home/rsat/rsat/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf
;	test_seq              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifspeak_seq
; Directories
;	output                        	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/
;	oligos_6nt_mkv4_m1            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m1/
;	oligos_6nt_mkv4_m2            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m2/
;	oligos_6nt_mkv4_m3            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m3/
;	oligos_6nt_mkv4_m4            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/
;	oligos_6nt_mkv4_m5            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m5/
;	positions_6nt_m1              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m2/
;	positions_6nt_m3              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m3/
;	positions_6nt_m4              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/
;	positions_6nt_m5              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m5/
;	oligos_7nt_mkv5_m1            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/
;	oligos_7nt_mkv5_m2            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m2/
;	oligos_7nt_mkv5_m3            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/
;	oligos_7nt_mkv5_m4            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/
;	oligos_7nt_mkv5_m5            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m5/
;	positions_7nt_m1              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m2/
;	positions_7nt_m3              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/
;	positions_7nt_m4              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m4/
;	positions_7nt_m5              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m5/
;	oligos_8nt_mkv6_m1            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/
;	oligos_8nt_mkv6_m2            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m2/
;	oligos_8nt_mkv6_m3            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m3/
;	oligos_8nt_mkv6_m4            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m4/
;	oligos_8nt_mkv6_m5            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m5/
;	positions_8nt_m1              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m1/
;	positions_8nt_m2              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/
;	positions_8nt_m3              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/
;	positions_8nt_m4              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/
;	positions_8nt_m5              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/
;	dyads_m1                      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/
;	dyads_m2                      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/
;	dyads_m3                      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/
;	dyads_m4                      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m4/
;	dyads_m5                      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m5/
; Output files
;	1nt_test_freq                 	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_archive.zip
;	dyads                         	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_2pssm                   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_asmb                    	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_m1_logo                 	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo.png
;	dyads_m1_logo_rc              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo_rc.png
;	dyads_m1_pssm_enrichment      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab
;	dyads_m1_pssm_enrichment_png  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.png
;	dyads_m1_pssm_site_distrib    	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab
;	dyads_m1_pssm_site_distrib_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png
;	dyads_m1_pssm_sites           	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab
;	dyads_m1_pssm_sites_genomic   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_genomic.bed
;	dyads_m1_pssm_sites_per_peak  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab
;	dyads_m1_pssm_sites_per_peak_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png
;	dyads_m1_tab                  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab
;	dyads_m1_tf                   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf
;	dyads_m1_vs_db_Schmidt_CEBPa_motif	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_Schmidt_CEBPa_motif.tab
;	dyads_m1_vs_db_Schmidt_CEBPa_motif_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_Schmidt_CEBPa_motif.html
;	dyads_m1_vs_db_jaspar_core_vertebrates	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_jaspar_core_vertebrates.tab
;	dyads_m1_vs_db_jaspar_core_vertebrates_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_jaspar_core_vertebrates.html
;	dyads_m1_vs_ref               	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_ref.tab
;	dyads_m1_vs_ref_html          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_ref.html
;	dyads_m2_logo                 	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_logo.png
;	dyads_m2_logo_rc              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_logo_rc.png
;	dyads_m2_pssm_enrichment      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab
;	dyads_m2_pssm_enrichment_png  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.png
;	dyads_m2_pssm_site_distrib    	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab
;	dyads_m2_pssm_site_distrib_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png
;	dyads_m2_pssm_sites           	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab
;	dyads_m2_pssm_sites_genomic   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_genomic.bed
;	dyads_m2_pssm_sites_per_peak  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab
;	dyads_m2_pssm_sites_per_peak_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png
;	dyads_m2_tab                  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab
;	dyads_m2_tf                   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf
;	dyads_m2_vs_db_Schmidt_CEBPa_motif	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_Schmidt_CEBPa_motif.tab
;	dyads_m2_vs_db_Schmidt_CEBPa_motif_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_Schmidt_CEBPa_motif.html
;	dyads_m2_vs_db_jaspar_core_vertebrates	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_jaspar_core_vertebrates.tab
;	dyads_m2_vs_db_jaspar_core_vertebrates_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_jaspar_core_vertebrates.html
;	dyads_m2_vs_ref               	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_ref.tab
;	dyads_m2_vs_ref_html          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_ref.html
;	dyads_m3_logo                 	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_logo.png
;	dyads_m3_logo_rc              	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_logo_rc.png
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;	positions_8nt_m3_pssm_sites_per_peak	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_sites_per_peak.tab
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;	positions_8nt_m3_tab          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tab
;	positions_8nt_m3_tf           	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf
;	positions_8nt_m3_vs_db_Schmidt_CEBPa_motif	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_Schmidt_CEBPa_motif.tab
;	positions_8nt_m3_vs_db_Schmidt_CEBPa_motif_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_Schmidt_CEBPa_motif.html
;	positions_8nt_m3_vs_db_jaspar_core_vertebrates	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates.tab
;	positions_8nt_m3_vs_db_jaspar_core_vertebrates_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates.html
;	positions_8nt_m3_vs_ref       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_ref.tab
;	positions_8nt_m3_vs_ref_html  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_ref.html
;	positions_8nt_m4_logo         	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_logo.png
;	positions_8nt_m4_logo_rc      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_logo_rc.png
;	positions_8nt_m4_pssm_enrichment	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_scan_mkv1_enrichment.tab
;	positions_8nt_m4_pssm_enrichment_png	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_scan_mkv1_enrichment.png
;	positions_8nt_m4_pssm_site_distrib	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_site_distrib.tab
;	positions_8nt_m4_pssm_site_distrib_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_site_distrib.png
;	positions_8nt_m4_pssm_sites   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites.tab
;	positions_8nt_m4_pssm_sites_genomic	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_genomic.bed
;	positions_8nt_m4_pssm_sites_per_peak	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_per_peak.tab
;	positions_8nt_m4_pssm_sites_per_peak_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_sites_per_peak.png
;	positions_8nt_m4_tab          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tab
;	positions_8nt_m4_tf           	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4.tf
;	positions_8nt_m4_vs_db_Schmidt_CEBPa_motif	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_Schmidt_CEBPa_motif.tab
;	positions_8nt_m4_vs_db_Schmidt_CEBPa_motif_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_Schmidt_CEBPa_motif.html
;	positions_8nt_m4_vs_db_jaspar_core_vertebrates	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_jaspar_core_vertebrates.tab
;	positions_8nt_m4_vs_db_jaspar_core_vertebrates_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_jaspar_core_vertebrates.html
;	positions_8nt_m4_vs_ref       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_ref.tab
;	positions_8nt_m4_vs_ref_html  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_ref.html
;	positions_8nt_m5_logo         	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_logo.png
;	positions_8nt_m5_logo_rc      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_logo_rc.png
;	positions_8nt_m5_pssm_enrichment	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_scan_mkv1_enrichment.tab
;	positions_8nt_m5_pssm_enrichment_png	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_scan_mkv1_enrichment.png
;	positions_8nt_m5_pssm_site_distrib	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_site_distrib.tab
;	positions_8nt_m5_pssm_site_distrib_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_site_distrib.png
;	positions_8nt_m5_pssm_sites   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites.tab
;	positions_8nt_m5_pssm_sites_genomic	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_genomic.bed
;	positions_8nt_m5_pssm_sites_per_peak	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_per_peak.tab
;	positions_8nt_m5_pssm_sites_per_peak_graph	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_sites_per_peak.png
;	positions_8nt_m5_tab          	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tab
;	positions_8nt_m5_tf           	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf
;	positions_8nt_m5_vs_db_Schmidt_CEBPa_motif	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_Schmidt_CEBPa_motif.tab
;	positions_8nt_m5_vs_db_Schmidt_CEBPa_motif_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_Schmidt_CEBPa_motif.html
;	positions_8nt_m5_vs_db_jaspar_core_vertebrates	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates.tab
;	positions_8nt_m5_vs_db_jaspar_core_vertebrates_html	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates.html
;	positions_8nt_m5_vs_ref       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_ref.tab
;	positions_8nt_m5_vs_ref_html  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_ref.html
;	positions_8nt_pssm_counts     	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.txt
;	positions_8nt_pssm_logo1      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m1.png
;	positions_8nt_pssm_logo2      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m2.png
;	positions_8nt_pssm_logo3      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m3.png
;	positions_8nt_pssm_logo4      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m4.png
;	positions_8nt_pssm_logo5      	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m5.png
;	positions_8nt_pssm_logo_rc1   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m1_rc.png
;	positions_8nt_pssm_logo_rc2   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m2_rc.png
;	positions_8nt_pssm_logo_rc3   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m3_rc.png
;	positions_8nt_pssm_logo_rc4   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m4_rc.png
;	positions_8nt_pssm_logo_rc5   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m5_rc.png
;	positions_8nt_pssm_sig        	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_sig_matrices.tf
;	positions_8nt_pssm_tf         	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.tf
;	small_summary                 	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_small_summary.html
;	small_summary_txt             	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/reports/peak-motifs_small_summary.txt
;	synthesis                     	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_synthesis.html
;	test_converted                	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400.fasta
;	test_purged                   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_maxlen400_purged_ml30_mis0.fasta
;	test_seq_coord                	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqcoord.bed
;	test_seqlen                   	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/reports/peak-motifs_timelog.txt
;	timelog_html                  	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/reports/peak-motifs_timelog.html
;	timetable                     	/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/reports/peak-motifs_timetable.txt

; 2014-09-03.192526
(cd $RSAT/public_html/tmp/wwwrun/2014/09/03 ;  zip -ryq peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_archive.zip peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M -x peak-motifs_archive.zip)