My apologies if this has been covered before but I am using Galaxy Main and
wonder if, when running TopHat, you can modify the mapping parameters used
by Bowtie? It seems that the full parameter list for TopHat pertains only
to the reads that aren't mapped by Bowtie (the reads spanning splice
junctions). Is there a way to access the full parameter list of Bowtie
through TopHat? Or perhaps run Bowtie directly, then feed this into a
TopHat run?

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