Dmr (Differentially Methylated Regions) Identification Software
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10.4 years ago
biostudent ▴ 30

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 • 11k views
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10.4 years ago

I think methylKit is a good option:

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

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10.4 years ago

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

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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

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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.

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10.4 years ago
Björn ▴ 670

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.

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

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

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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.

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10.4 years ago
Bioch'Ti ★ 1.1k

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

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6.8 years ago
hongbo919 ▴ 30

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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