RSAT - peak-motifs result

Analysis: E3F (03/04/2025 15:36)

Command

peak-motifs  -v 1 -title E3F -i $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin end -offset -200 -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/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s

Sequence composition

Sequence composition (test sequences)

Nb of peaks: 1
Total seq. size: 1 kb
Min length: 708 bp
Mean length: 708 bp
Max length: 708 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: 1
Total seq. size: 1 kb
Min length: 708 bp
Mean length: 708 bp
Max length: 708 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	Not a single significant pattern	[dyads_test_vs_ctrl]

Discovered motifs (with motif comparison)

Motif discovery

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 E3F -i $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin end -offset -200 -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/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s

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_04_03.153605 ; Job done 2025_04_03.153605 ; Job started 2025_04_03.153605 ; Job done 2025_04_03.153605 ; Job started 2025_04_03.153610 ; Job done 2025_04_03.153610 ; Job started 2025_04_03.153610 ; Job done 2025_04_03.153610

Warning: Not a single pattern was found in file tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/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/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab

Warning: Not a single pattern was found in file tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/results/dyads_test_vs_ctrl/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab

Warning: Discovered motif file does not exist tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/results/discovered_motifs/peak-motifs_motifs_discovered.tf

Error: OpenInputFile: File tmp/www-data/2025/04/03/peak-motifs.2025-04-03.153602_2025-04-03.153602_fxHm7s/results/discovered_motifs/peak-motifs_motifs_discovered.tf does not exist.
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Not a single discovered motif. Reducing the order of the Markov model may increase sensitivity.