Question: Dmr (Differentially Methylated Regions) Identification Software
3
gravatar for biostudent
6.8 years ago by
biostudent30
biostudent30 wrote:

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.

software methylation • 8.7k views
ADD COMMENTlink modified 3.2 years ago by hongbo91920 • written 6.8 years ago by biostudent30
4
gravatar for Charles Warden
6.8 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

I think methylKit is a good option:

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

ADD COMMENTlink written 6.8 years ago by Charles Warden7.9k
2
gravatar for Devon Ryan
6.8 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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

ADD COMMENTlink written 6.8 years ago by Devon Ryan96k

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

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Charles Warden7.9k
1

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.

ADD REPLYlink written 6.8 years ago by Devon Ryan96k
1
gravatar for Björn
6.8 years ago by
Björn660
Germany
Björn660 wrote:

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.

ADD COMMENTlink written 6.8 years ago by Björn660

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

ADD REPLYlink written 6.8 years ago by Devon Ryan96k

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

ADD REPLYlink written 6.8 years ago by Björn660
3

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.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Devon Ryan96k
0
gravatar for Bioch'Ti
6.8 years ago by
Bioch'Ti1.0k
France (Avignon)
Bioch'Ti1.0k wrote:

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

ADD COMMENTlink written 6.8 years ago by Bioch'Ti1.0k
0
gravatar for hongbo919
3.2 years ago by
hongbo91920
hongbo91920 wrote:

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! :)

ADD COMMENTlink modified 2.9 years ago • written 3.2 years ago by hongbo91920
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