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  • #1

    Determining alignment rate for Tophat

    Hi,

    I was just wondering if anyone could tell me the best way to find the overall alignment rate for a tophat run. I like how Bowtie outputs the alignment stats with an overall alignment rate as stdout, and am looking for something similar for Tophat.

    I found that in the tophat_out/logs folder I can find the overall alignment rate for the left and right reads separately. Can I just average these to find the overall alignment rate?

    Thanks for any suggestions.
    Tags: alignment rate, ngs, tophat
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