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Coryza · 02-07-2014, 12:44 AM

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 6.bt 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?

02-07-2014, 12:44 AM	#1
Coryza Member Location: Enschede Join Date: Feb 2014 Posts: 29	'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 6.bt 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?