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Old 06-02-2010, 02:13 AM   #2
Location: Ithaca, NY

Join Date: Apr 2010
Posts: 39

Is bowtie in your PATH? You can either copy the bowtie executable to the same dir as tophat, or `export PATH=$PATH:/location/of/bowtie`. Exporting the path would need to be done every time you log on, or it could be added to the rc file of the shell you use (~/.bashrc for bash, ~/.zshrc for zsh, etc). You could also try a symbolic link - in the tophat directory, `ln -s /path/to/bowtie bowtie`
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