Hi Daniel,
Thanks for reporting this issue - we have done some testing here and can
duplicate your results.
We are still reviewing options about how to address this, including
Galaxy wrapper modifications and possibly more. The issue has to do with
how certain variables are passed in the wrapper and interpreted in the
command string. If you are interested, write me back to let me know and
I can send you a link to the development ticket you can track (once
created).
Back to how to do this sort of analysis - yes, "aln -n" is a type of
mismatch parameter. And ideally setting this would result in a
mismatch-free alignment. Instead it returns no results:
Maximum edit distance (aln -n): "0"
and
Fraction of missing alignments given 2% uniform base error rate (aln -n): "0"
As a work-around, we have found that making the the Fraction variable
very small achieves a close approximation of mismatch-free alignments on
our test sets. This is by no means a guarantee, but pending future
changes, these are the recommended form settings:
Maximum edit distance (aln -n): "0"
and
Fraction of missing alignments given 2% uniform base error rate (aln -n):
"0.00001"
Thank you for your patience while we worked out exactly what was going
on. Hopefully the temporary work-around will allow you to continue with
your research,
Jen
Galaxy team
On 3/2/13 11:44 AM, Daniel Sher wrote:
Hello,
We have a sample containing several bacterial species and we want to
uniquely map RNA-seq reads to the genomes of each of our organisms to
get the expression patterns of each organism separately. We tried to
use BWA in Galaxy with the "edit distance" (aln -n in the command line
version) set to 0 but none of the reads were mapped (all had the SAM
tag set to "4'). This is an artifact since running BLAST with some of
the sequences showed that they have 100% identity to one of our
genomes and not any others, so they should map uniquely.
When running BWA with the number of mismatches set to between 1-5 >90%
of our reads were mapped, and the number of mapped reads increased
with the mismatch number so that seems to be working OK.
Does the "aln -n" option really determine the number of mismatches?
Any ideas why BWA will not run well in Galaxy using --n=0?
Thanks
Daniel
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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