Hi Guys,
a question about multiple alignment with bwa and coverage. Let's say I use the flag -n 2 when running bwa samse and for a couple of (not necessarely mated ) reads I get the following situation
read1: maps on region A and in XA report a second alignment on region B
read2: maps on region B and in XA report a second alignment on region C
When I run the pileup of this alignment file (e.g. with samtools) will I get a coverage 2 on region B?
thanks for helping
a question about multiple alignment with bwa and coverage. Let's say I use the flag -n 2 when running bwa samse and for a couple of (not necessarely mated ) reads I get the following situation
read1: maps on region A and in XA report a second alignment on region B
read2: maps on region B and in XA report a second alignment on region C
When I run the pileup of this alignment file (e.g. with samtools) will I get a coverage 2 on region B?
thanks for helping