Hi Ed

Given a BAM file e.g. x.bam the application is looking for the file x.bam.bai in the same directory. It sounds this is the case? If you create the index file with samtools :


samtools index x.bam

then it will create x.bam.bai. You could try re-creating the index with samtools.

Regards
Tim

On Wed, 20 Apr 2011, Edward Dudley wrote:

I'm trying to read a BAM file into Artemis (release 13.0 for Mac), and
keep getting an error message that it can't find my bam.bai file.

I have 454 reads that were converted to BAM format using Galaxy, and I
can visualize the alignment against an E. coli genome using the UCSC browser that is built in. So I downloaded the .bam and index file (which I changed the extension to .bam.bai), and loaded up an E. coli genome into Artemis. When I try to load in the .bam file, I get an error message that says it can't find the .bam.bai. Both files are in the same folder, and except for the extension are saved with identical names. Any suggestions?

Thanks.

Ed

Edward G. Dudley, Ph.D.
Assistant Professor of Food Science
The Pennsylvania State University
326 Food Science Building
University Park, PA 16802
(814) 867-0439
http://www.foodscience.psu.edu/Department/Faculty/Dudley.html


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