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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