0
$\begingroup$

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?

$\endgroup$
4
  • $\begingroup$ 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? $\endgroup$
    – M__
    Nov 26 '20 at 6:13
  • 1
    $\begingroup$ 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). $\endgroup$
    – Devon Ryan
    Nov 26 '20 at 10:38
  • $\begingroup$ Can you tell us anything about the data that you want to use to identify such patterns? $\endgroup$ Nov 27 '20 at 21:12
  • $\begingroup$ 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. $\endgroup$ Dec 1 '20 at 16:58

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.