Hello Clare,

An example of how to sort a SAM file is included in the workflow from #2 on this FAQ (it can be imported and the sort modified as needed):
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq

If you are starting with a BAM file, convert BAM->SAM, then after sorting, back with SAM->BAM, using tools in the group "NGS: SAM Tools".

Best regards,

Jen
Galaxy team

On 12/4/11 9:45 PM, Clare Sloggett wrote:
Hi galaxy users,

Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy?

I think this has probably been discussed before, sorry. I just want to
check I haven't missed anything, since sibling tools from e.g. the
samtools and picard suites are wrapped.

Thanks,
Clare


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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