Hello,<br><br>I am getting what seems to me to be strange results using two different mapping tools in Galaxy.  I am mapping illumina RNA-seq data and with tophat, while setting # alignments to 1, I get around 15-20% reads mapping.  And when I use bwa, I am getting around 75% reads mapping.  My reference is a collection of ESTs so the strength of tophat being a spliced read mapper is probably not being utilized, but I am surprised by the difference in the number of reads mapping between the two.  Any thoughts?<br>
<br>Austin<br>