Are There Any Alternatives To Methylkit For Methylation Call ?

Question

[samsara]

I have RRBS data. I tried to find differentially methylated promoter region using methylKit, but it reported promoter regions that does not have any base methylated. The result does not seem reliable. Are there any alternative to methylKit for methylation call ?

Answer 1

[Devon Ryan]

You have a couple options. Firstly, there's the BSseq package in Bioconductor. I've only used that for whole genome BS data, but if you google around a bit on the Bioconductor email list you'll find some tips for using it with RRBS data. There's also BiSeq, which I've never used so I can't say anything else about. Finally, there's Methyl-Pipe, which I've also never used but also does alignment I think.

There are actually a few more packages on Bioconductor, so have a look there as well.