Hi all,
is there any way to recompute mapping qualities of single reads? In my case, I want to trim reads after mapping, so I cut sequence and (base calling) qualities appropriately and adjust the CIGAR string. Further, this should (in most cases i guess) lead to an increased mapping quality, as most of the trimmed bases are mismatches.
Can I recompute mapping quality without performing the mapping step again?
Thank you!!
is there any way to recompute mapping qualities of single reads? In my case, I want to trim reads after mapping, so I cut sequence and (base calling) qualities appropriately and adjust the CIGAR string. Further, this should (in most cases i guess) lead to an increased mapping quality, as most of the trimmed bases are mismatches.
Can I recompute mapping quality without performing the mapping step again?
Thank you!!
Comment