Identifying peaks of similar enrichment from ChIP-seq?

Question

[umbch]

Hi All,

There are so many tools which are used to examine differential regions and peaks called out from tools such as MACs for ChIP-seq data. However I have some confounding results from a recent ATAC-seq and would quite bizarrely like to identify peaks of similar enrichment between all my samples rather than differential peaks. Does anybody know of any tools which may help me identify these peaks from MACs?

I am very new to the bioinformatics side of things so apologies if this is a pretty mundane question.

Answer 1

[jared.andrews07]

I'd probably just use any of the differential peak enrichment tools and select for peaks that don't meet whatever p-value/signal/FDR/magnitude threshold you use.

It'd be pretty easy to do this with MAnorm, diffBind, or csaw (and many others), I'd think.