Can you tell me which version of Tophat
In the next couple weeks we'll update to the newest version, v1.1.2
and Cufflinks is being used
The most recent version, v0.9.2
and whether the Tophat you have uses a GFF or GTF file to help it
find splices (this is an option I believe)?
Not currently, but we'll add this features in the next couple weeks.