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Old 02-07-2014, 01:43 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You might have to type the full PATH to bowtie2. As an aside, it's going to be a lot of hassle to deal with bioinformatics programs on windows (try to borrow someone's Mac).

Also, unless your organism doesn't have much splicing, you'll probably get better results using tophat2.
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