The way to compare ChIPSeq peaks enrichment level in different samples

Question

[Pinji Lei]

I have ChIPSeq data from four samples, and I want to compare peaks enrichment level among those samples.

Answer 1

[Ian]

You could try MACS2 bdgdiff: https://github.com/taoliu/MACS/wiki/Call-differential-binding-events

Here are some other tools: http://andre-rendeiro.me/2015/04/03/chipseq_diffbind_analysis/

Answer 2

[Devon Ryan]

Not exactly peak enrichment, but a convenient and unbiased method is bamFingerprint from deepTools.