search

biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

ChIP-seq WT vs mutants comparison #93

Open nermah1 opened 3 years ago

nermah1 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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