Thanks Peter. I've added your patch to the Trello card tracking incorporation
of community contributions to the Bowtie wrapper:
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
> Hello Alexander
> I've made some changes to our local copy of the bowtie tool files
> (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing
> bowtie's stderr output and adding it as an additional history item (here the
> statistics in this output is used as input to a local tool).
> I've attached patches to the tool in case they're any use to you.
> (As an aside and more generally: I'm not sure how to manage these local
> customisations in the longer term - what do other people on this list do?)
> HTH, best wishes, Peter
> On 25/02/13 11:29, Alexander Kurze wrote:
>> I am using the bowtie-wrapper on my locally installed galaxy server to
>> align reads. However I missing the stats read-out. Is there any
>> possibility to include statistics about unaligned reads?
>> If I use bowtie vi comman line I get following output:
>>> bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam
>> End-to-end 2/3-mismatch full-index search: 01:00:21
>> # reads processed: 12084153
>> # reads with at least one reported alignment: 9391748 (77.72%)
>> # reads that failed to align: 2692405 (22.28%)
>> Reported 30293838 alignments to 1 output stream(s)
>> The output should be normally saved in the stderr but unfortunatly the
>> stderr is somehow deleted after the alignment job is done in bowtie
>> under galaxy.
>> Any idea how I can still access the stats?
>> Alexander Kurze, DPhil
>> University of Oxford
>> Department of Biochemistry
>> South Parks Road
>> Oxford, OX1 3QU
>> United Kingdom
>> Tel: +44 1865 613 230
>> Fax:+44 1865 613 341
>> Please keep all replies on the list by using "reply all"
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> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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