Hi Daniel,

Yes, "aln -n" is a type of mismatch parameter. Would you like to share a history so we can take a look at all exact settings and provide feedback? From the history panel (far right, top corner), click on the gear icon, select "Share or Publish" from the menu, then click on the share button (first one). Copy the link and send that back in an email to just me, not the entire list, to keep your data private.


If you are running this on a local instance, maybe try to see if you can duplicate on the public Main server, both to rule out local install issues and to help with sharing. Small sample test/s that demonstrate the issue would be fine.
http://usegalaxy.org

I will watch for your email,

Hopefully we can help!

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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Jennifer Hillman-Jackson
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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:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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please use the interface at:

 http://lists.bx.psu.edu/

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