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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Choose sensible defaults for segmentation. #120

Open alexg9010 opened 6 years ago

alexg9010 commented 6 years ago

It makes most sense to have segmentation in the pigx_bsseq reports with K=4 or K=3, since this is what we would expect. see https://github.com/BIMSBbioinfo/Strategies_for_analyzing_BS-seq/blob/master/segmentation_tools/MethylSeekR_vs_methylKit_ESC.Rmd#segment-using-methylkit

alexg9010 commented 6 years ago

Maybe in the same run we have to add the parameters to the settings file.

Blosberg commented 6 years ago

@alexg9010 , is this essential functionality that we can implement quickly, or can I put this on the wishlist for now?