RSAT - peak-motifs result

Analysis: M12 (05/06/2025 16:11)

Command

peak-motifs  -v 1 -title M12 -i $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8

Sequence composition

Sequence composition (test sequences)

Nb of peaks: 80
Total seq. size: 37 kb
Min length: 249 bp
Mean length: 467.688 bp
Max length: 1201 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Sequence composition (ctrl sequences)

Nb of peaks: 17743
Total seq. size: 9629 kb
Min length: 201 bp
Mean length: 542.692 bp
Max length: 1201 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Discovered motifs (by algorithm)

motif discovery

oligos_6nt_test_vs_ctrl

Not a single significant pattern

[oligos_6nt_test_vs_ctrl]

oligos_7nt_test_vs_ctrl

Not a single significant pattern

[oligos_7nt_test_vs_ctrl]

dyads_test_vs_ctrl

dyads_test_vs_ctrl_m1	assembly: ccgnnnnnnnnnnccc (sig=0.24; e-value=0.58)	RC: gggnnnnnnnnnncgg
dyads_test_vs_ctrl_m2	assembly: tggnnnnnnnnnnnnnnnnnnncca (sig=0.24; e-value=0.58)	RC: tggnnnnnnnnnnnnnnnnnnncca
dyads_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

Discovered motifs (with motif comparison)

Motif discovery

Motif 1 dyads_test_vs_ctrl_m1

k-mer sig=0.24; evalue=0.58

ycCCGsybcccrhvbCCCyw

WRGGGVBDYGGGVRSCGGGR

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 30 (37.50%)
Max nb of predicted sites per peak: 5
(CHLRE_06g256300v5)
Mean nb of predicted sites per peak: 1.43

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 dyads_test_vs_ctrl_m2

k-mer sig=0.24; evalue=0.58

msTGgsCgvsyygsrscgsCCtygCCAcm

KGTGGCRAGGSCGSYSCRRSBCGSCCASK

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 22 (27.50%)
Max nb of predicted sites per peak: 2
(CHLRE_14g624350v5)
Mean nb of predicted sites per peak: 1.14

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif locations (sites)

Predicted sites on test peaks (all motifs)

[tab]
[bed]

Motif comparisons

Word significance table
Word comparisons		[tab] [html] [heatmap]
Comparisons between discovered motifs
Discovered motifs versus discovered motifs		[ Discovered motif(s): tf ] [ table: html txt ] [ alignments (logo): html text ] [ clustering: html ] [ graph: gml (for CytoScape) ]

Command:  peak-motifs  -v 1 -title M12 -i $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8

Logs and parameter files

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

Publications

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568.

; Job started 2025_06_05.160725 ; Job done 2025_06_05.160725 ; Job started 2025_06_05.160726 ; Job done 2025_06_05.160726 ; Job started 2025_06_05.160854 ; Job done 2025_06_05.160854 ; Job started 2025_06_05.160855 ; Job done 2025_06_05.160855

Warning: Not a single pattern was found in file tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl.tab

Warning: Not a single pattern was found in file tmp/www-data/2025/06/05/peak-motifs.2025-06-05.160723_2025-06-05.160723_glKVi8/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab