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Old 10-19-2012, 09:18 AM   #1
chris
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Default On/off target rate for whole exome data

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?
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Old 10-19-2012, 11:20 AM   #2
swbarnes2
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Quote:
Originally Posted by chris View Post
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.
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Old 10-19-2012, 12:25 PM   #3
Bukowski
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Quote:
Originally Posted by chris View Post
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.
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Old 10-21-2012, 01:06 PM   #4
chris
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Great. Thanks.
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Old 01-15-2013, 01:14 PM   #5
desaila
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@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!
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Old 01-21-2013, 01:56 AM   #6
chris
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Sure, its:

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