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Old 10-24-2014, 06:44 PM   #6
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
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But the command options you included for bowtie2 example that you ran directly are not the same as what TopHat used.

The parameters used in TopHat are the defaults for bowtie2 is what you were saying. My apologies.

Last edited by GenoMax; 10-24-2014 at 06:58 PM.
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