Thanks it is working now.

Best wishes,

Alex


On Wed, Feb 27, 2013 at 9:35 AM, Peter Briggs <peter.bri...@manchester.ac.uk
> 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:
>
>> Hello,
>>
>> 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?
>>
>> Thanks,
>>
>> Alex
>>
>> --
>> 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
>>
>>
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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
>
>
>


-- 
Alexander Kurze
70 Sunningwell Road
Oxford, OX1 4SX

Tel:   +44 1865-243-609
Mobile:  +44 7962-425-865
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