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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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Import of programs from pre-methpipe #48

Closed andrewdavidsmith closed 8 years ago

andrewdavidsmith commented 10 years ago

Can people tell me which of the programs in pre-methpipe have already been fully imported into methpipe so I can remove them from my repo?

mengzhou commented 10 years ago

I think it's only methcounts2

andrewdavidsmith commented 10 years ago

Not bsrate2 or allelicmeth2?

bdecato commented 10 years ago

Allelicmeth2 as well On Aug 11, 2014 8:10 PM, "Andrew Smith" notifications@github.com wrote:

Not bsrate2 or allelicmeth2?

— Reply to this email directly or view it on GitHub https://github.com/smithlabcode/methpipe/issues/48#issuecomment-51857908 .

bdecato commented 9 years ago

I think the only two remaining to integrate are bsrate2 and roimethstat2. We may benefit from rewriting bsrate to include analysis of bisulfite conversion along reads and potentially throw away reads that are low conversion.

bdecato commented 8 years ago

roimethstat2 imported. Still need to implement bsrate2 and add option for merged-symmetric CpGs to levels2.

bdecato commented 8 years ago

@andrewdavidsmith I am testing bsrate2, and there are a few changes I was wondering what the motivation for was.

1) We no longer accumulate the "overhanging" bases and warn that a nonzero number of reads mapped to the very end of a chromosome. Why was this removed?

2) bsrate2 has (potentially debug) output that prints the read counts to standard error. Is this something that should be removed, or did you want to clean up the presentation and put it in an auxiliary file??

It looks like most changes are just formatting. I removed bsrate2's identify_chromosomes function in favor of smithlab_cpp's and tested it: it produces identical output to the original.

bdecato commented 8 years ago

Per our conversation, it seems bsrate2 has previously been integrated/is not important to integrate. All of the "2" programs in pre-methpipe have been incorporated now!