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On/off target rate for whole exome data

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  • 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?

  • #2
    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.

    Comment


    • #3
      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.

      Comment


      • #4
        Great. Thanks.

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        • #5
          @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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          • #6
            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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