Body: <p>Suppose I generate a DNA sequence of the following pattern.</p>
  <p>AAGTC</p>
  <p>And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence</p>
  <p>AAAGGC</p>
  <p>Where there was an insertion error in the first position, second position and deletion in the third position and no error in the final position.</p>
  <p>I currently know the error pattern but is there a way to automatically identify the error patterns and annotate them?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-26T06:13:33.437Z
Comments.Text: Hi and welcome. Could you please edit your post to be clearer, speciically are you obtaining errors in the allele calling? What data pipelines are you using?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-26T10:38:51.013Z
Comments.Text: Stated differently, "I want to perform pairwise alignment and get the resulting CIGAR string." The CIGAR string is the error pattern (note that there may be a number of equal possibilities).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-27T21:12:18.323Z
Comments.Text: Can you tell us anything about the data that you want to use to identify such patterns?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-01T16:58:38.290Z
Comments.Text: The original message is a sequence of length 150. After being passed through a channel with insertion, deletion and substitution errors(or no error) it could have slightly different length.
Comments.UserDisplayName: Matthew Jones
Tags: <phylogenetics><ngs>
Title: DNA sequence error annotation
ThreadText: # DNA sequence error annotation
  
  (Asked by: username_0 on 2020-11-26)
  
  Suppose I generate a DNA sequence of the following pattern.
  
  AAGTC
  
  And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence
  
  AAAGGC
  
  Where there was an insertion error in the first position, second position and deletion in the third position and no error in the final position.
  
  I currently know the error pattern but is there a way to automatically identify the error patterns and annotate them?
  
  **Tags:** phylogenetics, ngs
  
  > **Comments:**
  > **username_1**: Hi and welcome. Could you please edit your post to be clearer, speciically are you obtaining errors in the allele calling? What data pipelines are you using?  
  > **username_2**: Stated differently, "I want to perform pairwise alignment and get the resulting CIGAR string." The CIGAR string is the error pattern (note that there may be a number of equal possibilities).  
  > **username_3**: Can you tell us anything about the data that you want to use to identify such patterns?  
  > **username_0**: The original message is a sequence of length 150. After being passed through a channel with insertion, deletion and substitution errors(or no error) it could have slightly different length.  
  
  ---
  
  ## 0 answers
  
  