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On/off target rate for whole exome data

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  • chris
    replied
    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

    Leave a comment:


  • desaila
    replied
    @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!

    Leave a comment:


  • chris
    replied
    Great. Thanks.

    Leave a comment:


  • Bukowski
    replied
    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.

    Leave a comment:


  • swbarnes2
    replied
    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.

    Leave a comment:


  • chris
    started a topic On/off target rate for whole exome data

    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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