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:
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.
J.