Body: <p>Looking at the sample <a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark/PE_report.html" rel="nofollow noreferrer">report</a> from <a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark/" rel="nofollow noreferrer">Bismark webpage</a>, there are two sections: <em>Cytosine Methylation</em> and <em>Cytosine Methylation after Extraction</em>. However even after reading <a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf" rel="nofollow noreferrer">User Guide</a>, I still cannot understand the difference between these two sections.</p>
  
  <p>As far as I understand this, <em>Cytosine Methylation</em> section shows summary statistics about Cytosine Methylation in sequenced data and <em>Cytosine Methylation after Exctraction</em> shows summary statistics after a Methylation calling, but is not the Methylation calling already part of the first section?</p>
  
  <p>My question therefore is: What is the difference between these two sections of Bismark report?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-15T10:12:12.317Z
Comments.Text: 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)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-21T20:37:46.333Z
Comments.Text: I was also looking for an answer to the same question and found this issue. have a look at this post https://github.com/FelixKrueger/Bismark/issues/245
Comments.UserDisplayName: SrivastavaS
Tags: <methylation>
Title: Bismark report before and after Cytosine Methylation Extraction
ThreadText: # Bismark report before and after Cytosine Methylation Extraction
  
  (Asked by: username_0 on 2018-12-11)
  
  Looking at the sample [report](https://www.bioinformatics.babraham.ac.uk/projects/bismark/PE_report.html) from [Bismark webpage](https://www.bioinformatics.babraham.ac.uk/projects/bismark/), there are two sections: *Cytosine Methylation* and *Cytosine Methylation after Extraction*. However even after reading [User Guide](https://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf), 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?
  
  **Tags:** methylation
  
  > **Comments:**
  > **username_1**: 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)  
  > **username_2**: I was also looking for an answer to the same question and found this issue. have a look at this post https://github.com/FelixKrueger/Bismark/issues/245  
  
  ---
  
  ## 0 answers
  
  