MethylDackel implementation

[bazyliszek]

Is it also possible to use MethylDacker files output instead of Bismark? https://github.com/dpryan79/MethylDackel
Maybe there is a way that DMRichR-compatible cytosine reports from methyldackel already?
In the Bismark cytosine report file, you have the following columns: "chromosome, position, strand, count methylated, count non-methylated, C-context, trinucleotide context". Methyldackel bedGraph file already contains columns 1, 2, 3 and 4.

By the way one of the link is not active in the repro: https://github.com/FelixKrueger/Bismark/tree/master/Docs#optional-genome-wide-cytosine-report-output

[ben-laufer]

Hi @bazyliszek, the cytosine reports are processed by DMRichR::processBismark(), which uses bsseq::read.bismark(). I'm not familiar with MethylDackel, but I'd recommend having a look over the "File formats section" of the bsseq::read.bismark() documentation to learn more. You can always fork DMRichR and modify DMRichR::processBismark().

[bazyliszek]

Thank you for your thoughts. @wassimsalam01 forked it and will have a look further https://github.com/wassimsalam01/DMRichR We found that Bismarck behaved a bit different from MethylDackel so we were a bit concerned, and also because of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465269/