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Old 10-19-2011, 08:56 PM   #1
komais
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Location: china

Join Date: Apr 2011
Posts: 5
Default Questions about bwa aln -n and -o

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.
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