Jo,

Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to a BAM file.


Ryan


On 3/25/11 10:35 AM, Jochen Seggewiß wrote:
Hi!

Thank you for your reply.

So that means, I should convert the csfasta & qual to fastq, map it with
Bowtie, get an SAM, convert it to BAM and then index that BAM?
How can I index BAM using GALAXY?
I haven´t found a way to get a BAM directly from GALAXY using csfasta &
qual as input files.

Best regards

Jo

Am 3/25/2011 3:13 PM, schrieb Jim Robinson:
Hi Jo,

To short-circuit confusion I'll jump in here.  I'm the developer of
IGV and igvtools,  the sorting and indexing for SAM files was added
long ago, even before indexed BAM files were possible from Java
programs.   The recommendation now is to convert to BAM and index
that,  although SAM files still work.   If the galaxy community would
like the SAM option I'm happy to have igvtools wrapped as a module,
and will help with that.

BTW,  I also have some code (xml) to wrap IGV itself as a Galaxy
visualizer,  contributed to me by a user.  As I don't have a private
Galaxy installation I'm unable to test it myself, but can make it
available if anyone is interested.

Jim


Hello!

I convert SOLiD csfasta- and qual-files to fastq-files and map those
against Hg19 (Bowtie).
I would like to use the resulting sam-files in the IGV browser (Broad
Institute).
Therefore, the sam-file need to be sorted an indexed. This could be
done using the “igvtools”.
However, it would be nicer if this sorting and indexing could be done
automatically using GALAXY.
I guess that it is certainly possible – but I do not know how.
Could anybody let me know how it works and what function I have to
use, respectively?
How can I sort the sam-file the correct way?

Thank you in advance.

Best regards

Jo
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