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?


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