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Old 02-07-2014, 12:44 AM   #1
Location: Enschede

Join Date: Feb 2014
Posts: 29
Default 'bowtie2' is not recognized.

Hi all,

I'm currently trying to use bowtie2 to map our RNAseq data to the mRNA reference / chromosomes reference. Building indexes went ok, however when trying to use bowtie2 -p 1 -x [path to indexes] [fastq file] > [sam file] it says 'bowtie2' is not recognized as an internal or external command, operable program or batch file.

I'm using the cmd on windows. Anyone who can help me out here?
Coryza is offline   Reply With Quote