[Bowtie2] Not recognized on Windows.

[Puhekupla]

I'm trying to run bowtie2 to align my sequence data. Bowtie2 says its better to run the bowtie2 file instead of the wrapper bowtie2-align directly. However when trying to run the bowtie2 on windows it says "is not recognized as an internal or external command, operable program or batch file.". Running bowtie2-align works, but I do have problems there that commands --un-conc --al-conc are not recognized.

Anyone has solutions for this?

Thanks,

[TiborNagy]

The error message said path of bowtie2 not in the PATH environment variable.