On/off target rate for whole exome data

chris · 10-19-2012, 09:18 AM

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 · 10-19-2012, 11:20 AM

Quote:

Originally Posted by 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?

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

Bukowski · 10-19-2012, 12:25 PM

Quote:

Originally Posted by 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?

Don't worry - perfectly acceptable figures there.

chris · 10-21-2012, 01:06 PM

Great. Thanks.

desaila · 01-15-2013, 01:14 PM

@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 · 01-21-2013, 01:56 AM

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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10-19-2012, 09:18 AM	#1
chris Member Location: Dundee, Scotland Join Date: Apr 2008 Posts: 52	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?

01-21-2013, 01:56 AM	#6
chris Member Location: Dundee, Scotland Join Date: Apr 2008 Posts: 52	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

10-21-2012, 01:06 PM	#4
chris Member Location: Dundee, Scotland Join Date: Apr 2008 Posts: 52	Great. Thanks.

01-15-2013, 01:14 PM	#5
desaila Junior Member Location: Boston Join Date: Oct 2010 Posts: 7	@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!