Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper: https://trello.com/c/TdYxdbkm Best, J. 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:
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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