Greetings—

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 basic

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.

Thanks

Mary E. Davis, Ph.D.

Professor

Department of Physiology & Pharmacology

West Virginia University Health Sciences Center

PO Box 9229

Morgantown, WV  26506-9229