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Old 09-07-2011, 09:04 AM   #6
kwicher
Junior Member
 
Location: Cambridge

Join Date: Jan 2011
Posts: 7
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I somehow made it:
I made a bash script which first export the PATH with directories to tophat,bowtie, and samtools; and then runs the tophat.

I am running this script from within qsub with single quotes

THanks fall al suggestions
K
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