RSAT - peak-motifs result

Analysis: MEnavajowhite2_Up3_W3 (26/05/2025 09:01)

Command

peak-motifs  -v 1 -title MEnavajowhite2_Up3_W3 -i $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/peak-motifscontrol_seq -markov auto -disco oligos,dyads,positions -nmotifs 10 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_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/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF

Sequence composition

Sequence composition (test sequences)

Nb of peaks: 23
Total seq. size: 16 kb
Min length: 247 bp
Mean length: 674.391 bp
Max length: 701 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: 41359
Total seq. size: 27124 kb
Min length: 201 bp
Mean length: 655.805 bp
Max length: 701 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

oligos_7nt_test_vs_ctrl_m1	assembly: aaaccac (sig=0.55; e-value=0.28)	RC: gtggttt
oligos_7nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

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

oligos_8nt_test_vs_ctrl

Not a single significant pattern

[oligos_8nt_test_vs_ctrl]

dyads_test_vs_ctrl

Not a single significant pattern

[dyads_test_vs_ctrl]

Discovered motifs (with motif comparison)

Motif discovery

Motif 1 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.55; evalue=0.28

yaaAaCCaCdy

RHGTGGTTTTR

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

footprintDB-plants

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor yaaAaCCaCdy

AT1G76870:MA1367.1:JASPAR AT1G76870/MA1367.1/JASPAR D 11 0.7857 0.833 0.655 NA NA

NF_CO:EEAD0014:EEADannot NF_CO/EEAD0014/EEADannot D 8 0.7273 0.885 0.644 NA NA

MYB46:MYB46_2:ArabidopsisPBM MYB46/MYB46_2/ArabidopsisPBM D 10 0.9091 0.700 0.637 NA NA

Total matches= 21 (18 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: 10 (43.48%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr21g0314251)
Mean nb of predicted sites per peak: 1.40

[ 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) ]
Discovered motifs versus transcription factor databases
Motifs versus footprintDB-plants database		[ table: html txt ] [ alignments (logo): html text ] [ graph: gml (for CytoScape) ]

Command:  peak-motifs  -v 1 -title MEnavajowhite2_Up3_W3 -i $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/peak-motifscontrol_seq -markov auto -disco oligos,dyads,positions -nmotifs 10 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_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/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF

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_05_26.084808 ; Job done 2025_05_26.084808 ; Job started 2025_05_26.084808 ; Job done 2025_05_26.084808 ; Job started 2025_05_26.085545 ; Job done 2025_05_26.085545 ; Job started 2025_05_26.085546 ; Job done 2025_05_26.085546

Warning: Not a single pattern was found in file tmp/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/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/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/results/oligos_8nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_8nt_test_vs_ctrl.tab

Warning: Not a single pattern was found in file tmp/www-data/2025/05/26/peak-motifs.2025-05-26.084806_2025-05-26.084806_cUwMUF/results/dyads_test_vs_ctrl/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab

RSAT - peak-motifs result

Analysis: MEnavajowhite2_Up3_W3 (26/05/2025 09:01)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results