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Old 09-26-2014, 08:27 AM   #39
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,125

You are trying to run the program from the current folder which is the wrong folder (did you read about the concept of relative paths at the Korf UNIX site? This is an extremely important concept to learn, when you are new to command line).

Based on your file listing try (from the directory where you provided the long list)

I do not remember if the e_coli data comes with the program. If it is there in the bowtie2 folder then you can omit (/you_need_to_provide_path_to/) part.

$ bowtie2-2.2.3/bin/bowtie2 -a -v 2 /you_need_to_provide_path_to/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT

$ cd bowtie2-2.2.3
$ bin/bowtie2 -a -v 2 /you_need_to_provide_path_to/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
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