Re: [Artemis-users] BAM in Artemis

2011-04-20 Thread Tim Carver 

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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Re: [Artemis-users] BAM in Artemis

2011-04-20 Thread Torsten Seemann 

 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.


I think the .bam file needs to be SORTED too (by reference coordinates)
before indexing. Chances are it already is sorted (as it was used with USCS)
but just in case:

% samtools sort original.bam original-sorted   # will
create original-sorted.bam
% samtools index original-sorted.bam

NOTE that for the sort command, you don't put the .bam suffix ... it does it
itself (ech).

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA
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