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.ku...@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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
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