On/off target rate for whole exome data

[chris]

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?

[swbarnes2]

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?

Actually, that's about what the people selling the kits promise, so you are fine.

[Bukowski]

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?

Don't worry - perfectly acceptable figures there.

[chris]

Great. Thanks.

[desaila]

@chris -- would you care to share your command line for bowtie2? I'm running into a slightly worse issue, performance wise, and am curious how you're doing it!

[chris]

Sure, its:

bowtie2 --threads 4 -q --sensitive --end-to-end --phred33 -x /db/bowtie2/Hsapiens68 -1 fastq_file1 -2 fastq_file1 -S out.sam