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narrowPeak or summits.bed for HOMER motif finding

Hello,

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.

Thank you

motif motiffinding homer macs bedformat
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updated by Nitin Narwade 168 • | written by buffealo 13

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.

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written by Nitin Narwade 168

Thank you. What I don't understand is that is it the difference between summits.bed and .narrowPeak files?

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written by buffealo 13

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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written by Nitin Narwade 168

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