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MD string for second reads
Hi
When I excute mappy with paired ends like
aligner.map(seq1,seq2, MD=True):
MD string for second reads is wrong. for example for 100nt length perfect match, it reports. 0T2A0G1C0T0C0A0T0T1T1T0T0G0C0C1A1G0C0T0G0G0A0G0T0G0C1G0T0G0G0T0G0T0G0A1C0T0C0G0G0C0T0C0A0C0T0G0C0A1C0C0C0C0C0A0A0C0C0C1C0A0C0T1C0C0C0A0G2T1A0A1C0G0A1T1T0C0C0T0G0C0C
I think, it maybe that second string is not reverse complemented when generating MD string. (I put read FR oriented as instructed and mapping just works fine.)
Thanks in Advance.