I was testing different parameters of tophat2 recently. But I found that changing of some parameters has no effect, because they are fixed in the tophat source code (python).
Tophat 2 can pass parameters to Bowtie 2 by using Bowtie 2 option name prefixed with "--b2-". Parameter
--b2-L is for setting the length of seed substrings, and it affects sensitivity and speed. It's hard-coded to
20. Another parameter
--b2-gbar is hard-coded to
If anyone is also running tophat with non-default parameter, I think this should be brought to their attention. I also wonder why the developers fix this values (although they work very well in most cases).