Answers.Body: <p>You'd be best off by starting with <code>-rfg</code> and <code>-rdg</code> as is and reverting bismark's change of <code>--score-min</code> back to the default for bowtie2. That alone will allow for much longer indels. If that still doesn't suffice, then I'd play around more with <code>--score-min</code> before messing with the gap open/extend penalties. If you do need to play with those, then increase the gap open penalty and decrease the gap extension to 1. Do check that the resulting alignments aren't nonsense though!</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-04T03:38:22.933Z
Answers.Text: With the bismark default `--score-min`, `-rdg`, and `-rfg` settings, it appears that the maximum sized indel identifiable with my read length is 3bp. I changed both `-rdg` and `-rfg` to a gap open/extension of (1,1) and the maximum length I can detect is 14bp. I will try modifying `--score-min` only. It's a fine line to walk, detecting the longest possible insertions while keeping the alignment clean!
Answers.UserDisplayName: Ben D.
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-03T18:30:18.183Z
Answers.LastActivityDate: 2017-08-03T18:30:18.183Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I am interested in identifying indels in whole genome bisulfite sequencing data (76bp paired end). Currently, I do this by setting the <code>-rfg</code> and <code>-rdg</code> affine gap penalty scores for bowtie2 to more permissive values than the default 5+3N and mapping using the bisulfite sequencing alignment wrapper, bismark.</p>
  
  <p>My question is, what values of <code>-rfg</code> and <code>-rdg</code> will allow me to identify longest possible indels without sacrificing alignment quality? Is it better to set the affine penalty to zero with a high penalty for initially opening an indel (ex. 8+0N)? Or is it better to keep the initial penalty low and having a nonzero penalty for extension (ex. 2+1N)?</p>
  
Tags: <ngs><phylogenetics><read-mapping><methylation><indel>
Title: Best way to detect long insertions in bisulfite sequencing data?
ThreadText: # Best way to detect long insertions in bisulfite sequencing data?
  
  (Asked by: username_0 on 2017-08-02)
  
  I am interested in identifying indels in whole genome bisulfite sequencing data (76bp paired end). Currently, I do this by setting the `-rfg` and `-rdg` affine gap penalty scores for bowtie2 to more permissive values than the default 5+3N and mapping using the bisulfite sequencing alignment wrapper, bismark.
  
  My question is, what values of `-rfg` and `-rdg` will allow me to identify longest possible indels without sacrificing alignment quality? Is it better to set the affine penalty to zero with a high penalty for initially opening an indel (ex. 8+0N)? Or is it better to keep the initial penalty low and having a nonzero penalty for extension (ex. 2+1N)?
  
  **Tags:** ngs, phylogenetics, read-mapping, methylation, indel
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2017-08-03. Score: 3 | Accepted answer
  
  You'd be best off by starting with `-rfg` and `-rdg` as is and reverting bismark's change of `--score-min` back to the default for bowtie2. That alone will allow for much longer indels. If that still doesn't suffice, then I'd play around more with `--score-min` before messing with the gap open/extend penalties. If you do need to play with those, then increase the gap open penalty and decrease the gap extension to 1. Do check that the resulting alignments aren't nonsense though!
  
  > **Comments:**
  > **username_0**: With the bismark default `--score-min`, `-rdg`, and `-rfg` settings, it appears that the maximum sized indel identifiable with my read length is 3bp. I changed both `-rdg` and `-rfg` to a gap open/extension of (1,1) and the maximum length I can detect is 14bp. I will try modifying `--score-min` only. It's a fine line to walk, detecting the longest possible insertions while keeping the alignment clean!  
  
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