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  • RPKM and duplicate read question

    we're working on mapping rnaseq short reads and wanted to get an idea of the current trends with which people are addressing these two main issues:

    1. what is the consensus on including or excluding cloned
    reads (reads which map to two or more places on the reference) specifically when looking at RNA-Seq in the context of gene
    expression analysis (I believe in NGS with DNA, cloned reads need to
    be excluded, perhaps also in de novo assembly of transcriptome using
    RNA -Seq)?

    2. Is RPKM still the accepted metric for expressing gene expression or
    if not what is the alternative?

    would be cool to see what the people out there are doing...

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