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Old 06-16-2010, 09:05 AM   #3
john_mu
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Location: Stanford, CA

Join Date: May 2010
Posts: 88
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"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18"

That is wrong

You should point the the bowtie-base, rather than the directory.

eg. something like

"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18/genome"
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