How to separate chip-seq peaks which are enriched for known TFs motifs from given list of peaks

Question

[Naresh D J]

Dear All,

I have a list of enhancer marks in terms of peaks file from chip-seq data (three column, chr, start, end) and run motif analysis using HOMER software (http://homer.salk.edu/homer/). It did gave few known and de novo enriched motifs. I want to identify the peaks which are enriched with these TFs motifs from the initial list of peaks.

Does anybody has ideas/suggestions to achieve this? Is it possible at all?

Thank you.

[jotan]

How about FIMO?

[Fidel]

I second that. You can run FIMO in your list of peaks to know which ones have the motif.

Answer 1

[Naresh D J]

There is a script in HOMER itself for finding the instances of the enriched motifs in the input of chip-seq peaks. "annotatepeaks.pl"

[ivivek_ngs]

You can use HOMER motif finder for the same, for finding both de novo and known motifs as well.

Answer 2

[ivivek_ngs]

You can also use C-SCAN for chip-seq data by taking into account the refseq id for the peaks if they are already annotated. This will give you a single output of which TFs are likely to be common regulators of the genes from the peaks.