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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