methylation analysis pipelines?

[saketkc]

Brad,

Any plans to incorporate methylome analysis pipelines? I am thinking of using bcbio-nextgen architecture to come up with one. Wondering if it would be a duplication of efforts?

However, I am not sure if this is a 'wishlisted' feature from the community.

[chapmanb]

Saket;
Thanks for checking in. This is something we'd like to have been haven't started any work to integrate it yet. @jnhutchinson has done most of the methylation work in our group and use Bismark for mapping (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) and BisSNP (https://sourceforge.net/projects/bissnp/) for calling, alongside BSeQC (https://code.google.com/p/bseqc/).

We'd be happy to accept any contributions if you have time to work on this. Thanks again.

[chapmanb]

Saket;
Thanks again. I added this to todo list as something we can work on in the future. Definitely happy to accept contributions if you end up working on this.

[saketkc]

I am working on this. The pace is going to be slow, though.

[jnhutchinson]

Saket, do let me know if I can be of any help. I likely wont' be much help with the actual implementation but I'm happy to serve as a guinea pig for trial runs.

Best,
John

[saketkc]

Sure, John!

[lpantano]

Hi @saketkc,

I am implementing some code for RRBS data. For now it is outside bcbio, but with a very similar structure so it should be easy to integrate it in the future. I just wanted to follow up with you to know if you have any update from your side. @jnhutchinson's pipeline is based on trim_galore, bismark and bissnp with some middle steps for filtering and bam cleaning. I don't know if you are using the same tools or completely different tools?

thanks in advance!

[saketkc]

Hi @lpantano,

Unfortunately I did not make a headstart with this. I do use the same tools, but outside bcbio. They are implemented in python too, but do not follow bcbio structure at all.

[lpantano]

Thanks for the feedback. If we end up implementing in bcbio will post here. And maybe from that it would be easier to have your comments for best practices.
Right now is here: https://github.com/lpantano/ASMfinder. Still not functional, hope to get it working during this week. It has all the parallelization with ipython (same way bcbio has).