Jeremy, > 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?
Not all Bowtie parameters can be modified when running Tophat. Which parameters are you looking to modify and why? > 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). This should not be the case. For instance, documentation for the max-multihits discusses multiple hits when mapping reads junctions/segments: http://tophat.cbcb.umd.edu/manual.html If you're seeing different results, it may be a bug that could be discussed with the Tophat authors: tophat.cuffli...@gmail.com > Is there a way to access the full parameter list of Bowtie through TopHat? Not currently. > Or perhaps run Bowtie directly, then feed this into a TopHat run? I don't think this is possible b/c Tophat uses the reads that map initially to build the coverage islands and then uses these islands to generate an index of potential splice junctions. Best, J.
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