Best software to identify differentially methylated regions in Chipseq data?

Question

[madkitty]

I'd like to hear opinions of those using chip seq methylation data.

What is the best software to find differentially methylated regions in chipseq data?

[TriS]

@madkitty...not sure what you mean for "chip seq methylation data"...chip seq or methylation? are you trying to integrate them? what have you tried so far? which kind of methylation data do you have? also, writing in bold doesn't give you a faster answer..

[madkitty]

I meant CHIPSeq data .. oops :)

Answer 1

[Devon Ryan]

You can't identify differentially methylated regions from ChIPseq data. You can from MeDIPseq, though.