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  • RPKM calculation

    Hi:
    Apologies for asking a very simple question. I could not find a reference and I had to ask here.

    Mortazavi et. al - RPKM calculation

    RPKM = 10^9 x C/NL

    what is the significance of 10^9.

    Is this the total number of bases in genome? I thought it is ~3billion bp.

    thanks
    Adrian

  • #2
    The formula to calculate RPKM (reads mapping to the genome per kilobase of transcript per million reads sequenced) should be:
    RPKM=(number of mapping reads)*1000bp*1 million reads/[(length of transcript)*(number of total reads )].
    Then you can find that 10^9 is correspond to 1000bp transcript multiple 1 million reads.

    Hope it can help you.

    feixue1039

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