I have peaks generated by MACS2 and I am wondering if I should give summits.bed or narrowPeak to HOMER findMotifsGenome.pl and annotatePeaks.pl as an input.
Generally, I prefer the 200bp region around the peak summit for motif enrichment analysis. You can adjust this width based on average peak size OR based on your domain knowledge about the protein of your interest.
Thank you. What I don't understand is that is it the difference between summits.bed and .narrowPeak files?
Well a simplest difference I can tell is the summits.bed has information of a peak where the score (protein binding intensity) is maximum in the peak whereas the narrowPeak file has complete peak boundary. If you look at the summits.bed you can see it reports a peak with width/distance 1bp. That means this is the region (of peak) where the protein binding intensity rich it's maximum. Therefore every peak should have its own summit.
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