Dmr (Differentially Methylated Regions) Identification Software

Question

[biostudent]

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.

Answer 1

[Charles Warden]

I think methylKit is a good option:

https://code.google.com/p/methylkit/

Answer 2

[Devon Ryan]

You might try bsseq. Whatever you do, don't use a Fisher's test.

[Charles Warden]

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

[Devon Ryan]

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.

Answer 3

[Björn]

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.

[Devon Ryan]

I'll reiterate my "whatever you do, don't use a Fisher's test" comment from above.

[Björn]

Can you explain your reasoning? Nevertheless, the fisher-test is optional in that script.

[Devon Ryan]

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.

Answer 4

[Bioch'Ti]

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

Answer 5

[hongbo919]

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! :)