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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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