Hi everyone,
I used BWA to map my paired end sequencing data. The length of read is 74bp. I would like to allow up to 3 mismatches in one read (no seed needed). I just set "bwa aln -n 3". Is this the correct setting for my purpose?
When I checked the mapped sam file (tag MD:Z), I saw more mismatches than three. So I am confused about mismatch settings in BWA. Can anybody help me?
Thanks!
I used BWA to map my paired end sequencing data. The length of read is 74bp. I would like to allow up to 3 mismatches in one read (no seed needed). I just set "bwa aln -n 3". Is this the correct setting for my purpose?
When I checked the mapped sam file (tag MD:Z), I saw more mismatches than three. So I am confused about mismatch settings in BWA. Can anybody help me?
Thanks!
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