Hi!
I have peak file (3 column bed file) from a ChIP-seq experiment and I want to identify the transcription factor motifs that are present in these peaks and also which motifs are co-occurring.
Is their any approach/tool through which I can get this done. I know for identification of motifs it is quite straight forward to use any motif identification tool such as gimme motifs, meme etc, but the challenge is how to identify co-occurring motifs or compute them.
Thank you
2 answers
You could start with this paper: "Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices." They have a link to a sourceforge site to download some software.
There are also a lot of references in this paper about software that evaluates cooccurence: http://bib.oxfordjournals.org/content/early/2013/08/15/bib.bbt053.abstract (disclosure: I am an author).
See this paper.
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Ming Tommy Tang
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