Question: Dmr (Differentially Methylated Regions) Identification Software
3
gravatar for biostudent
5.5 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 • 7.8k views
ADD COMMENTlink modified 22 months ago by hongbo91920 • written 5.5 years ago by biostudent30
4
gravatar for Charles Warden
5.5 years ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

I think methylKit is a good option:

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

ADD COMMENTlink written 5.5 years ago by Charles Warden6.6k
2
gravatar for Devon Ryan
5.5 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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

ADD COMMENTlink written 5.5 years ago by Devon Ryan90k

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 5.5 years ago • written 5.5 years ago by Charles Warden6.6k
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 5.5 years ago by Devon Ryan90k
0
gravatar for Björn
5.5 years ago by
Björn650
Germany
Björn650 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 5.5 years ago by Björn650

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

ADD REPLYlink written 5.5 years ago by Devon Ryan90k

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

ADD REPLYlink written 5.5 years ago by Björn650
2

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 5.5 years ago • written 5.5 years ago by Devon Ryan90k
0
gravatar for Bioch'Ti
5.5 years ago by
Bioch'Ti1000
France (Avignon)
Bioch'Ti1000 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 5.5 years ago by Bioch'Ti1000
0
gravatar for hongbo919
22 months 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 18 months ago • written 22 months ago by hongbo91920
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