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  • to use multi-core in Tophat

    Does anyone know how to use parallel computing in Tophat?

    The option "-p" is not working for me -- my command is:
    "tophat -p 10 -r 100 hg19 mate1.fa mate2.fa" but there's still only one CPU processing.

    Any idea?

    Thanks a lot,

    Iris
    Last edited by IrisZhu; 07-30-2010, 10:10 AM.

  • #2
    TopHat does some steps along the way which are not parallellized, you probably monitored TopHat's CPU usage during one of those steps. Try monitoring TopHat during the alignment steps and see if it isn't using several threads.

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