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  • 75mer mapping with BOWTIE

    Hey all,

    I'm looking for some input on tuning BOWTIE for 75mer RNA-seq reads from mus - any suggestions? I'm currently allowing only unique hits, and using 68bp as seed length, but that may be too conservative.

    Best,
    Johannes Waage
    Uni. of Copenhagen

  • #2
    Hi Johannes,

    That's certainly reasonable; I suggest doing a series of runs using your target data but also using the -u parameter to cut the job off after a certain number of reads so that it doesn't take forever. Doing several such runs with different sets of parameters (but the same -u) should help you determine the sweet spot w/r/t speed and sensitivity.

    Ben

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    • #3
      Hi,

      We are doing this routinely. We typically use the -v 2 option and use an index made from both the genome and splice junctions with 69 nt on either side of the junction. Surprisingly, we get a very large fraction of reads that map uniquely using these parameters.

      Brent

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      • #4
        Hi Johannes:
        How do you deal with exon junctions? some exons will be shorter than 75bps. Try tophat?

        Xuying

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        • #5
          Can you tell me what reference are you using?
          -drd

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          • #6
            Originally posted by drio View Post
            Can you tell me what reference are you using?
            mm9 combined with a combinatorial exon-exon DB (142mers, requiring overlap of 4nt)

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