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  • oxydeepu
    replied
    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

    Leave a comment:


  • sdriscoll
    replied
    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.

    Leave a comment:


  • oxydeepu
    replied
    Sorry for incomplete question. I meant from the bowtie output file.

    Deepak

    Leave a comment:


  • sdriscoll
    replied
    the map file?

    Leave a comment:


  • oxydeepu
    started a topic Bowtie alignment distribution

    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

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