Hi all,
I've some human exome data, which I've aligned with bowtie2 as bwa doesn't work (see this post).
Using samtools flagstat I can see ~98% of reads map to the genome. However, only about 60% of those are on-target with 40% off-target. That doesn't seem great.
What kind of on/off-target rates do others see?
I've some human exome data, which I've aligned with bowtie2 as bwa doesn't work (see this post).
Using samtools flagstat I can see ~98% of reads map to the genome. However, only about 60% of those are on-target with 40% off-target. That doesn't seem great.
What kind of on/off-target rates do others see?
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