bowtie command giving error

[Sharmi]

Hi,
I am new to bioinformatics and linux and I have downloaded bowtie linux86 and the source files. I get the following error
cbil@cbil-desktop:~/bowtie-linux/bowtie-1.0.1$ reads/e_coli_1000.fq
bash: reads/e_coli_1000.fq: Permission denied

Can someone please help me?

Thanks,
Sharmi

[dpryan]

You'd do well to get a book on basic Linux usage (even if you're using OSX, most of that would apply).

cbil@cbil-desktop:~/bowtie-linux/bowtie-1.0.1$

This is equivalent to opening the "~/bowtie-linux/bowtie-1.0.1" directory in Windows Explorer (under Windows) or Finder (on a Mac) in that it just says where on the system you are.

reads/e_coli_1000.fq

You're now telling the system to execute the fastq file, which doesn't really make any sense. The actual error originates because the fastq file isn't set as being executable. Even if it were, however, that still wouldn't work since fastq files aren't programs. You want something of the form:

cbil@cbil-desktop:~/bowtie-linux/bowtie-1.0.1$ ./bowtie e_coli reads/e_coli_1000.fq