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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