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sartorlab / methylSig

R package for DNA methylation analysis
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Is it possible to use bedgraphs from methyldackel that are not destranded? #55

Closed bioinfoMMS closed 7 months ago

bioinfoMMS commented 7 months ago

I have a quick question on using the output bedgraphs from methyldackel as input for methylsig. If I run methyldackel without their destranding option (--mergecontext), can bsseq/methylsig destrand it for me?

For instance, doing this:

bsseq_destranded = bsseq::read.bismark( files = files, colData = data.frame(row.names = c('test1','test2')), rmZeroCov = FALSE, strandCollapse = TRUE )

where the files are bedgraphs from Methyldackel that have not been destranded.

Thanks!

rcavalcante commented 7 months ago

Hi,

Yes, I use the bedgraphs from methyldackel all the time for methylSig. In reality, methylSig uses the bsseq::read.bismark function to read in files, and that function handles the bedgraphs just fine.

Thanks, Raymond

bioinfoMMS commented 7 months ago

But does it do the destranding? or does that have be done by Methyldackel beforehand?

rcavalcante commented 7 months ago

I think it's more expensive to do the destranding in R than with methyldackel so I'd recommend doing it with methyldackel first.