ChIP-seq WT vs mutants comparison

[nermah1]

Hi, I really appreciate your efforts making these tools.
I'm a quite new to this area and have a question rather than an issue.

I successfully completed jobs with epic and generated lists of peaks.
For simplicity, let's say I have WT H3K27me3 peaks and mutant H3K27me3 peaks.
WT H3K27me3 peaks were generated from epic using -t H3K27me3 -c H3 and greylist was already removed from the two lists.
Mutant H3K27me3 peaks were made in the same way.

Now the question is, if I wanna compare H3K27me3 of WT vs mutants, can I just re-run epic with these epic-generated result?

Or for this purpose, do you recommend using other programs such as Diffbind or DESeq maybe?

[endrebak]

Thanks!

To answer your question, I do not know. I think biostars would be a better fit for your question :)

Also, have you tried epic2? It is much better XD

[nermah1]

Ok! Thanks for the quick response. And yes, I will update my scripts to epic2 after my lab meeting lol