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 - -
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.
On Mon, Feb 25, 2013 at 1:29 PM, Alexander Kurze <
> 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
> 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
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