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Old 06-02-2010, 05:37 AM   #4
Location: Ithaca, NY

Join Date: Apr 2010
Posts: 39

It looks like tophat really wants the indexes and reads to be in the same directory. You should try copying either the index files or the reads to the other directory, or both to the same, and run again. Maybe copy both to /tmp if you have the disk space, then transfer the resulting output to your users' /home?
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