RSAT - peak-motifs

Pipeline for discovering motifs in massive ChIP-seq peak sequences.

References

  1. Thomas-Chollier, M., Herrmann, C., Defrance, M., Sand, O., Thieffry, D. and van Helden, J. (2011). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets Nucleic Acids Research doi:10.1093/nar/gkr1104, 9. [Open access]
  2. 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. [PMID 22836136]

Peak Sequences
Title (mandatory)
Peak sequences (mandatory)     Paste your sequence (fasta format)

Or select a file to upload (.gz compressed files supported)

   URL of a sequence file available on a Web server (e.g. Galaxy).


Mask 

Optional: control dataset for differential analysis (test vs control)

Control sequences     Paste your sequence (fasta format)

Or select a file to upload (.gz compressed files supported)

   URL of a sequence file available on a Web server (e.g. Galaxy).


Mask 

(I only have coordinates in a BED file, how to get sequences ?)


Output 
Note: email output is preferred for very large datasets or many comparisons with motifs collections

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