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?
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