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  • AsoBioInfo
    Member
    • Dec 2011
    • 37
    #1

    Insert mean size in *.rsem.sorted.bam.stats file

    Hello,

    I am just little confused about the inner mate difference needed for TopHat. The rsem.sorted.bam.stats file had been generated during RNA-sequencing. It have an insert mean of 173 bp. Paired-end data run on 50-mer.

    The value of option '-r' in TopHat will be 173 or only 73? I think, it should be 173 but I just want to be sure before I start further analysis.

    Thanks in advance!
    Aso
    Tags: -r option, insert mean, tophat
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