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.
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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"
You can use HOMER motif finder for the same, for finding both de novo and known motifs as well.
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.
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How about FIMO?
I second that. You can run FIMO in your list of peaks to know which ones have the motif.