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Old 02-07-2014, 12:44 AM   #1
Coryza
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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 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?
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