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