I tried to run an alignment using Bowtie2 and got this message-

format: bam, database: mm9
Could not locate a Bowtie index corresponding to basename 
"/galaxy/data/mm9/mm9canon/bowtie2_index/mm9canon" Error: Encountered internal 
Bowtie 2 exception (#1) Command: 
/galaxy/software/linux2.6-x86_64/pkg/bowtie2-2.1.0/bin/bowtie2-align --wrapper 

I imported Illumina fastq data, groomed them, and then did the analysis using 
the built-in index mouse, both full and male, and had the same error message.

I'm relatively new to this, and don't see what I missed.


Mary E. Davis, Ph.D.
Department of Physiology & Pharmacology
West Virginia University Health Sciences Center
PO Box 9229
Morgantown, WV  26506-9229

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