You can change the bowtie wrapper to save the stderr of the bowtie part.

The command line is (bowtie2_wrapper.py):
cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s'
Change it to something like:
cmd = 'bowtie2 %s -x %s %s %s 2> bowtie_stderr_filename | samtools view -Su - | samtools sort -o - - > %s'
Where bowtie_stderr_filename is a temporary filename.
And concat this before the stderr afterwards (of the whole command).

Hopefully, the official bowtie-wrapper will have this addition too.

Hagai



On Mon, Feb 25, 2013 at 1:29 PM, Alexander Kurze <alexander.kurze@bioch.ox.ac.uk> 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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