Looking at the sample report from Bismark webpage, there are two sections: Cytosine Methylation and Cytosine Methylation after Extraction. However even after reading User Guide, I still cannot understand the difference between these two sections.

As far as I understand this, Cytosine Methylation section shows summary statistics about Cytosine Methylation in sequenced data and Cytosine Methylation after Exctraction shows summary statistics after a Methylation calling, but is not the Methylation calling already part of the first section?

My question therefore is: What is the difference between these two sections of Bismark report?

  • $\begingroup$ Did you try contacting the authors of Bismark? It doesn't seem to be highly used, so I doubt we have here someone who could answer you. (If you find the answer, then post it here for others please) $\endgroup$
    – llrs
    Dec 15 '18 at 10:12
  • $\begingroup$ I was also looking for an answer to the same question and found this issue. have a look at this post github.com/FelixKrueger/Bismark/issues/245 $\endgroup$ Apr 21 '20 at 20:37

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