Hi Jen,

Thanks for this, belatedly!  And happy new year!

I think this will work for some of my cases but possibly not all,
since it looks like chromosomes are being sorted alphabetically. It
depends what the reference genome used was and what tools you're
planning to use after sorting as to whether this is ok.

I was initially just wondering why 'samtools sort' hadn't been wrapped
- not as a complaint, but since the various other samtools options
mostly seem to be already wrapped, I wondered if there was some
particular reason not to have this one. If I were to try to wrap
'samtools sort' myself is there some difficulty I should know about?

Thanks again,

On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> 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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