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

Question

[brentp]

I put up a guide here, feedback welcome.

[Devon Ryan]

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

[brentp]

Can't do iframes. Here is the link: https://github.com/brentp/450k-analysis-guide/blob/master/README.md

[Obi Griffith]

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

[brentp]

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

[Obi Griffith]

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

Answer 1

[Charles Warden]

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

[brentp]

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.

[Charles Warden]

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.