I searched for previous posts on this but the question below was not explicitly answered in the three threads I found.
So here goes:
The output from the "idxstats" command in samtools generates four values. What exactly does the last column (# unmapped reads) signify?
Is "idxstats" the best way to "count" mapped reads in BAM files?
Thanks in advance.
So here goes:
The output from the "idxstats" command in samtools generates four values. What exactly does the last column (# unmapped reads) signify?
Is "idxstats" the best way to "count" mapped reads in BAM files?
Thanks in advance.