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  • Muthukumar
    Member
    • Jan 2016
    • 11

    Read count

    Hello all,

    In a RNA-seq experiment , how to measure/count the reads which are produced for specific gene.
  • Michael.Ante
    Senior Member
    • Oct 2011
    • 127

    #2
    In general, you know where your gene is located (given by gene coordinates) and then count how many valid reads align to this region. There are a plethora of tools out there to do this job (htseq-count, featureCount, Cufflinks, rsem,....)
    Last edited by Michael.Ante; 03-22-2016, 11:59 PM. Reason: Typo

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