Are there any good DMR software available for running on data for DNA methylation data? Googling results in many different software, but I want to use something that you would recommend using that is easy to set up and run on methylation expression data obtained from WGBS.
I think methylKit is a good option:
You might try bsseq. Whatever you do, don't use a Fisher's test.
We have developed a few scripts to handle WGBS data:
https://github.com/bgruening/methtools
As a bonus we integrated them in Galaxy and it worked quite well for our reseachers.
There's no reason to expect methylation metrics at a given site to follow a hypergeometric distribution across biological replicates. This is effectively the same reason we use negative binomial distributions with RNAseq count data rather than just sequencing a single sample and assuming a Poisson distribution. While I don't think anyone has really nailed the perfect way to analyze bisulfite sequencing data, bsseq is a good step in the right direction.
Hi, Maybe you could start with reading this review paper: Analysing and interpreting DNA methylation data : http://www.nature.com/nrg/journal/v13/n10/full/nrg3273.html Best
Hi, we have developed a new software for de novo identification of DMRs from various BS-Seq data including WGBS. Maybe it is useful for you. http://fame.edbc.org/smart/ Best wishes! :)
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version 2.3.6
I was about to suggest BSmooth (which I admittedly haven't tried), but it appears that it actually uses bsseq:
http://rafalab.jhsph.edu/bsmooth/
http://genomebiology.com/2012/13/10/r83
Yeah, bsmooth is just the aligner. It's OK (you'll generally get both more true and false positives compared to bismark), but very slow.