Hi Ben,
I am confused how Bowtie deals with the quality scores when counting mismatches.
I noticed that there are two parameters related to this issue. First, -n/--seedmms <int> indicates the maximum mismatches in seed, meaning that if a hit with greater than the mismatch cutoff it will not be reported by Bowtie. And second, -e/--maqerr <int> indicates the maximum sum of quality scores allowed at the mismatched bases (is it right?). However, I don't know whether the two criteria are the same or complemental.
Further, the two measurements of mismatches are both counted in seed region. Even though the users can specify the seed length, I am wondering where does the seed locate: from the leftmost of a query (read) or a random region in the query.
Besides, there is another parameter -v <int>, which takes care the end-to-end mismatches, but does not consider the quality scores. Is it possible to make this consider the quality scores?
Best regards!
Xi
I am confused how Bowtie deals with the quality scores when counting mismatches.
I noticed that there are two parameters related to this issue. First, -n/--seedmms <int> indicates the maximum mismatches in seed, meaning that if a hit with greater than the mismatch cutoff it will not be reported by Bowtie. And second, -e/--maqerr <int> indicates the maximum sum of quality scores allowed at the mismatched bases (is it right?). However, I don't know whether the two criteria are the same or complemental.
Further, the two measurements of mismatches are both counted in seed region. Even though the users can specify the seed length, I am wondering where does the seed locate: from the leftmost of a query (read) or a random region in the query.
Besides, there is another parameter -v <int>, which takes care the end-to-end mismatches, but does not consider the quality scores. Is it possible to make this consider the quality scores?
Best regards!
Xi
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