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

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, Clare On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson <jen(a)bx.psu.edu&gt; 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 > > -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:  http://lists.bx.psu.edu/

Hi Carlos, Thanks! I didn't realise the conversion was doing that. In fact I want bam files (I'm also using GATK) so this is really helpful. Cheers, Clare On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto <carlos.borroto(a)gmail.com&gt; wrote: > Hi Clare, > > I ran into a similar question testing out GATK pipeline on Galaxy. My > solution was to always convert my SAM files to BAM. The wrapper also > sorts the final BAM file output and it does this using the known > 'samtools sort', which sorts chromosomes in the same order of the > reference genome. The reference genome can be automatically selected > by the build associated with the dataset or choose from the history. > > I haven't confirmed if a conversion from BAM to SAM would do the same thing. > > Hope it helps, > Carlos > > On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett <sloc(a)unimelb.edu.au&gt; wrote: >> 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, >> Clare >> >> On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson <jen(a)bx.psu.edu&gt; 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 >>> >>> >> >> >> >> -- >> E: sloc(a)unimelb.edu.au >> P: 03 903 53357 >> M: 0414 854 759 >> ___________________________________________________________ >> 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: >> >>  http://lists.bx.psu.edu/ > > -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759