Hi,
I aligned pair end reads using bwa aln -n 0.02 and 0.04. My expectation is there would be higher mapping rate using 0.04 than 0.02. However, I got more reads mapped to genome using 0.02 than 0.04.
The other phenomenon is when I run bwa aln specifying -o 0, I got a output file contain reads those are gapped aligned.
Can someone explain how these happened?
Thank you.
I aligned pair end reads using bwa aln -n 0.02 and 0.04. My expectation is there would be higher mapping rate using 0.04 than 0.02. However, I got more reads mapped to genome using 0.02 than 0.04.
The other phenomenon is when I run bwa aln specifying -o 0, I got a output file contain reads those are gapped aligned.
Can someone explain how these happened?
Thank you.