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  • #1

    Tophat 2.0.4 vs 2.0.6

    I'm mapping reads (around 20 mil avg 92bp in length) using tophat 2.0.4 and 2.0.6. 2.0.4 maps to around 91% while 2.0.6 maps to only 67%. Does anyone know what accounts for such a huge difference?

    Both tophats are run with default parameters and GTF files.

    Bowtie version: 2.0.0.7
    Samtools version: 0.1.18.0

    Thanks!
    Tags: None
  • #2
    Anyone have any idea as to what can account for this difference?

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