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  • Bowtie alignment distribution

    hi all,

    I have aligned my RNA-Seq reads to the reference genome using bowtie. Now i want to know where the reads are getting aligned from the map file - like is it coming from repetitive element or exon, etc.
    Please help. Thank you in advance.
    Deepak

  • #2
    the map file?
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

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    • #3
      Sorry for incomplete question. I meant from the bowtie output file.

      Deepak

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      • #4
        So the next step would be to use a tool like Cufflinks to quantify expression of genes in terms of some annotation - typically a GTF file from ensemble or UCSC's table browser. That and make a bedGraph of your alignments so you can view them in the UCSC genome browser.
        /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
        Salk Institute for Biological Studies, La Jolla, CA, USA */

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        • #5
          Thank you.

          Is there any other way we can figure out from the alignment output whether it is coming from an exonic region or repeat region.

          Cheers
          Deepak

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