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  • Bowtie Aligning failed 100%

    Hello,

    I am trying to use bowtie to align sanger human DNA reads on hg19. The command line I have used is:
    ./bowtie -p 1 -m 20 --best --sam hg19 ../Task/Source/454reads_test.fastq ../Task/Source/454reads_test.sam
    and I got the following report:
    # reads processed: 84205
    # reads with at least one reported alignment: 0 (0.00%)
    # reads that failed to align: 84205 (100.00%)
    No alignments

    The sequences seem unusually long, 300-400bases.
    And actually, I am not sure if I should use hg19 as prebuild index. There several indexes fir H. Sapian.

    Could any one please help me with this alignment?

    Thank you very much in advance.

    Heidi
    Last edited by HeidiLee; 08-05-2012, 01:46 AM.

  • #2
    I think I need to use BWA-SW for sequences with long lengths.
    I am still learning :0)

    Comment


    • #3
      Bowtie2, Blat, and Blast are also a possibilities.

      Whatever you choose, make sure you understand how it decides what to report. Bowtie was tuned for short reads, so it will not report matches if there are more than a few snps. It's also sensitive to where the snps fall in the read- snps at the 5' end are in the region it uses as an alignment seed and it can't handle more than 2 there.

      Bowtie2 lets you specify the minimum score to report a match in terms of the query length, which scales much better with increasing read lengths.

      Comment

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