Installing Bowtie on Windows 7

[niteesh.prasad]

Hi! I'm trying to install the Bowtie tool for my genomic processing class, but with no success.

I downloaded the windows 32 bit .zip file from sourceforge and unzipped it. Set the environment path and then tried to run a few simple commands from the command line.

The command I tried was:

bowtie -t e_coli reads/e_coli_1000.fq e_coli.map

It always gives me "Bowtie is an unrecognized command". I don't really know what to do to get this tool running. I'd appreciate the help!

[gringer]

It always gives me "Bowtie is an unrecognized command". I don't really know what to do to get this tool running. I'd appreciate the help!

If this were the exact error and you were using Linux, I would say you need to run './bowtie' rather than 'Bowtie'. However, I would guess that this is not the problem because I assume that the current directory is still in the default path for Windows, and that Windows is still case sensitive in file names.

The other "check the power cable is plugged in" solution is to make sure you're calling bowtie with the full directory location, and that all arguments including file names are quoted, for example:

C:\bowtiedata>"C:\Program Files\Bowtie\bowtie" -t "e_coli" "reads/e_coli_1000.fq" "e_coli.map"

I guess you could also add the bowtie directory to your PATH environment variable, but that seems to be getting more difficult to do with every new Windows version.

[Sorry if I'm a bit vague on this -- it's been a while since I've used a Windows computer as my main desktop or laptop]