RSA-tools - peak-motifs result

Analysis: ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps (06/09/2014 01:22)

peak-motifs  -v 1 -title ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db regulonDB tf $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -motif_db footprintDB tf $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN

motif discovery
oligos_6nt_mkv2	oligos_6nt_mkv2_m1 asmb: gatcaat (sig=1.90) RC: attgatc oligos_6nt_mkv2_m2 asmb: gatcaaa (sig=1.33) RC: tttgatc oligos_6nt_mkv2_m3 : (sig=) RC: oligos_6nt_mkv2_m4 : (sig=) RC: oligos_6nt_mkv2_m5 : (sig=) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	Not a single significant pattern	[positions_6nt]
oligos_7nt_mkv2	oligos_7nt_mkv2_m1 asmb: aggagta (sig=1.20) RC: tactcct oligos_7nt_mkv2_m2 asmb: attgatct (sig=0.70) RC: agatcaat oligos_7nt_mkv2_m3 asmb: attcacc (sig=0.09) RC: ggtgaat oligos_7nt_mkv2_m4 : (sig=) RC: oligos_7nt_mkv2_m5 : (sig=) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_7nt	Not a single significant pattern	[positions_7nt]
oligos_8nt_mkv2	oligos_8nt_mkv2_m1 asmb: agagggag (sig=0.86) RC: ctccctct oligos_8nt_mkv2_m2 asmb: aatttgat (sig=0.64) RC: atcaaatt oligos_8nt_mkv2_m3 asmb: acgcagaa (sig=0.32) RC: ttctgcgt oligos_8nt_mkv2_m4 asmb: aacttgat (sig=0.16) RC: atcaagtt oligos_8nt_mkv2_m5 : (sig=) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_8nt	Not a single significant pattern	[positions_8nt]
dyads	dyads_m1 asmb: attgatcnngatcaat (sig=16.99) RC: attgatcnngatcaat dyads_m2 asmb: caaaaaa (sig=1.97) RC: ttttttg dyads_m3 asmb: attgacnnngatcaat (sig=16.99) RC: attgatcnnngtcaat dyads_m4 asmb: taannnnnnnnnata (sig=1.08) RC: tatnnnnnnnnntta dyads_m5 asmb: gatcaaa (sig=3.33) RC: tttgatc	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]

Motif discovery
Motif 1   oligos_6nt_mkv2	taGATCAATrw WYATTGATCTA	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor taGATCAATrw FNR ECK120011229 R 8 0.4706 0.863 0.406 taGATCAA... ......TWRATCAA Total maches= 1		[ match table: html text ] [ alignments (logos): html text ]
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor taGATCAATrw 7424_HBP1_f1_HOCOMOCO_v9_ 7424_HBP1_f1_HOCOMOCO_v9_ D 6 0.4615 0.939 0.433 .....CAATrw CAATgr.. 6530_3a01_E_3D-footprint_20130124_ 6530_3a01_E_3D-footprint_20130124_ D 6 0.5455 0.896 0.489 .....CAATrw CAATtA 5763_SOX15_full_2_HumanTF_1.0_ 5763_SOX15_full_2_HumanTF_1.0_ D 8 0.4444 0.925 0.411 ...ATCAATrw ATCAATAm....... Total maches= 35 (32 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 6 (5.50%) Max nb of predicted sites per peak: 1  (?_gi|49175990|ref|NC_000913.2|_4011895_4011996_+) Mean nb of predicted sites per peak: 1.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_7nt_mkv2	TsAGGAGTAyw WRTACTCCTSA	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor TsAGGAGTAyw NarP ECK120011508 R 8 0.7273 0.789 0.574 ..AGGAGTAh. AGRRGTAK NarL ECK120011502 D 8 0.7273 0.764 0.555 .sAGGAGTA.. wakrrkTA Total maches= 2		[ match table: html text ] [ alignments (logos): html text ]
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor TsAGGAGTAyw 5131_YufM_DBTBS_1.0_ 5131_YufM_DBTBS_1.0_ D 8 0.7273 0.786 0.572 ..AGGAGTAh. ArGrGdws 5047_ZmHOX2a_1__Athamap_20091028_ 5047_ZmHOX2a_1__Athamap_20091028_ R 7 0.6364 0.825 0.525 TsAGGAG.... TTAGGAY 2780_PF0093.1_JASPAR_CORE_2009_ 2780_PF0093.1_JASPAR_CORE_2009_ D 6 0.5455 0.778 0.424 ...GGAGTA.. GGATTA Total maches= 7 (4 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 9 (8.26%) Max nb of predicted sites per peak: 1  (?_gi|49175990|ref|NC_000913.2|_939973_940074_+) Mean nb of predicted sites per peak: 1.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_8nt_mkv2	rwAGAGGGAGwS SWCTCCCTCTWY	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rwAGAGGGAGwS Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rwAGAGGGAGwS 6513_2v2t_A_3D-footprint_20130124_ 6513_2v2t_A_3D-footprint_20130124_ D 6 0.5000 0.860 0.430 .....GGGAGw. GGgAnT 6322_1svc_P_3D-footprint_20130124_ 6322_1svc_P_3D-footprint_20130124_ R 7 0.5833 0.829 0.483 .....GGGAGws GGGANNC 2711_PF0024.1_JASPAR_CORE_2009_ 2711_PF0024.1_JASPAR_CORE_2009_ D 7 0.5385 0.758 0.408 .....GGGAGws GGGAGGr. Total maches= 3		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 3 (2.75%) Max nb of predicted sites per peak: 1  (?_gi|49175990|ref|NC_000913.2|_281330_281431_+) Mean nb of predicted sites per peak: 1.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   dyads_m1	aaaTTGATctagATCAAwwt AWWTTGATCTAGATCAATTT	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor aaaTTGATctagATCAAwwt FNR ECK120011229 D 14 0.7000 0.948 0.663 ...TTGATctadATCAA... tTGaTywayATCAA Total maches= 1		[ match table: html text ] [ alignments (logos): html text ]
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor aaaTTGATctagATCAAwwt 3061_FNR_RegulonDB_7.5_ 3061_FNR_RegulonDB_7.5_ D 14 0.7000 0.948 0.663 ...TTGATctadATCAA... tTGaTywayATCAA 7440_HNF6_f1_HOCOMOCO_v9_ 7440_HNF6_f1_HOCOMOCO_v9_ R 13 0.6500 0.780 0.507 .......TctadATCAAwww WHWAARTCAATAW Total maches= 2		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 22 (20.18%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_4131663_4131764_+) Mean nb of predicted sites per peak: 1.91	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   dyads_m2	wtwTTGAystagATCAAtww WWATTGATCTASRTCAAWAW	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wtwTTGAystagATCAAtww FNR ECK120011229 R 14 0.7000 0.915 0.641 ...TTGAystagATCAA... TTGATRTWRATCAA Total maches= 1		[ match table: html text ] [ alignments (logos): html text ]
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wtwTTGAystagATCAAtww 3061_FNR_RegulonDB_7.5_ 3061_FNR_RegulonDB_7.5_ R 14 0.7000 0.915 0.641 ...TTGAystagATCAA... TTGATRTWRATCAA 1999_PB0144.1_JASPAR_CORE_2009_ 1999_PB0144.1_JASPAR_CORE_2009_ D 12 0.5000 0.839 0.420 ........stagATCAAtww swrsATCAATCr.... 2042_PB0188.1_JASPAR_CORE_2009_ 2042_PB0188.1_JASPAR_CORE_2009_ D 12 0.5000 0.832 0.416 ........stagATCAAtww sdrsWTCAATCr.... Total maches= 8 (5 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 32 (29.36%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_770360_770461_+) Mean nb of predicted sites per peak: 1.62	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   dyads_m3	ymGATCAAAtw WATTTGATCKR	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ymGATCAAAtw FNR ECK120011229 D 8 0.4706 0.863 0.406 ymGATCAA... ......wayATCAA Total maches= 1		[ match table: html text ] [ alignments (logos): html text ]
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ymGATCAAAtw 2526_MA0151.1_JASPAR_CORE_2009_ 2526_MA0151.1_JASPAR_CORE_2009_ D 6 0.5455 0.887 0.484 ...ATCAAA.. ATyAAA 1939_PB0082.1_JASPAR_CORE_2009_ 1939_PB0082.1_JASPAR_CORE_2009_ D 11 0.6471 0.799 0.517 ymGATCAAAtw ..wasATCAAAGg.... 6733_4euw_A_3D-footprint_20130124_ 6733_4euw_A_3D-footprint_20130124_ D 6 0.5455 0.883 0.481 ....TCAAAt. TcAAAg Total maches= 33 (30 more)		[ match table: html text ] [ alignments (logos): html text ]
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 12 (11.01%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_34015_34116_+) Mean nb of predicted sites per peak: 1.08	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db regulonDB tf $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -motif_db footprintDB tf $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN