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Old 09-25-2013, 10:36 AM   #1
Location: USA

Join Date: Jul 2011
Posts: 18
Default Software tools for comparing entire methylomes (WGBS)

Software tools for comparing entire methylomes (WGBS)

I am currently exploring the possibility of comparing entire methylomes of genets exposed to two different conditions.

There seem to be a few options as for software tools to map bisulfite-seq reads (Bismark), but the options for comparing entire methylomes don't seem to exist as a tools as of yet.

Essentially, I would like to model the work of Heyn et al. 2012. The details of their methods are available in supplemental materials.

Is there a less cumbersome way of achieving what they are doing? Are there any tools capable of this? What is the most efficient way of identifying differential methylation between two samples?

Thank you!

Last edited by anth; 09-25-2013 at 02:46 PM. Reason: My hasty post appeared to describe an experiment with an n of 1.
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Old 09-25-2013, 12:56 PM   #2
Devon Ryan
Location: Freiburg, Germany

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Do you really just have 2 samples? The normal reply would be to reference bsseq, but with just 2 samples I doubt any results would be meaningful. Why didn't you use biological replicates? You have absolutely no way of knowing if any differences are due to your treatment or are just normal variation.
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Old 09-25-2013, 02:47 PM   #3
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Thanks for your reply. The experiment has not been undertaken yet - but there will absolutely be biological replicates for each condition. I have edited the original post to correct this.
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Old 12-10-2013, 04:25 PM   #4
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Location: Los Angeles

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Hi anth,

My lab just published our WGBS toolbox and database, MethPipe/MethBase. We analyzed ~200 WGBS datasets (including the Heyn set you linked), calling single-base resolution methylation levels as well as identifying high-level methylation features like HMRs, allele-specific methylation, and PMDs. This should allow you to generate your own data, run it through our pipeline, and compare it to the public data knowing that you used the same methods.

You can find the paper at

The database and pipeline themselves (and a user manual) can be found here:

Let me know if you give it a try/have any questions. Good luck!
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