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Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data

I put up a guide here, feedback welcome.

450k methylation
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updated by Ram Ram • written by brentp brentp

Nice tutorial. I'd missed your Comb-p paper and will have to give it a read too.

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written by Devon Ryan Devon Ryan

Nice tutorial. Are you aware of any similar tutorials for the NGS version of this?

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written by Obi Griffith Obi Griffith

you mean for NGS DNA methylation analyses? if so, not yet, maybe in a few months.

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written by brentp brentp

Yeah. Exactly. Looking for good tutorials on analysis of WGBS and RRBS data. Will keep my eyes open.

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written by Obi Griffith Obi Griffith

1 answer

For those that are interested, there is also this tutorial on using COHCAP for analysis of 450k data:

http://www.nature.com/protocolexchange/protocols/2965

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written by Charles Warden Charles Warden

That's a great writeup that I hadn't seen. I have avoided packages like ChAMP (or whatever the capitalization is) and COHCAP because I felt that they had a lot of functions to just run, when I could do the same on my own with more control. On closer look COHCAP looks like it has some useful features, and IIRC, it has some nice stuff for relating methylation to expression that I'd like to look into.

By the way, re your intro statement, comb-p was out before COHCAP. Unfortunately, it hasn't seen much use.

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written by brentp brentp

Ok, thanks for letting me know. One annoying thing is that the Protocol Exchange listings don't seem to be designed with future edits in mind, but I will add a comment.

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updated by Ram Ram • written by Charles Warden Charles Warden

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