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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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allelicmeth: mirroring methcounts and bsrate #8

Closed bdecato closed 10 years ago

bdecato commented 10 years ago

methcounts will soon be updated to mirror bsrate's mechanism of keeping running tabulations of an entire chromosome's methylation counts and then computing all methylation levels when all the reads for that chromosome have been processed.

allelicmeth could benefit from this structure as well: instead of keeping tabulations of a chromosome's methylation counts, it could keep track of the 2-CpG methylation state counts ([0,0] [0,1] [1,0] [1,1]), and at the end of a chromosome could quickly calculate p-values for the allelic-ness of each pair of CpGs.

andrewdavidsmith commented 10 years ago

This should be easily closed by finishing the allelicmeth2 in my pre-methpipe repo.

bdecato commented 10 years ago

Finished.