Forum:Isaac aligner with unmapped reads in BAM file
I was using the Isaac aligner for analyze the human sample. When I view the results of bam files from the Isaac v4, I see the unmapped reads.
I’m wondering which criteria or values (i.e., the number of mismatches in the read, base quality, mapping quality …etc) decide to reads as unmapped reads? I think there is no mismatch percentage cutoff for mapped reads.
I would appreciate a lot if you could help me out.
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