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Old 07-30-2010, 08:38 AM   #1
Location: Maryland

Join Date: Jul 2010
Posts: 25
Default 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,


Last edited by IrisZhu; 07-30-2010 at 10:10 AM.
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Old 08-04-2010, 12:39 PM   #2
Thomas Doktor
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Location: University of Southern Denmark (SDU), Denmark

Join Date: Apr 2009
Posts: 105

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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