I am new to the field of RNA-Seq analysis. I'd be very greatful if somene could help me with the following issue:

I'm using the Galaxy Main plattform and would like to run Tophat2 on RNA-Seq data from rat. However in Main under Tophat2 there are only built-in human and mouse genomes, while a lot more genomes are vailable under Tophat for Illumina.
I tried to import the rat genome sequence using the built-in UCSC Table browser, however I only managed to get a full genome as one FASTA file with all the different sequences. After mapping to this genome I can't see any hits when I click "display at UCSC main" on accepted hits. So I assume that the mapped reads do not conform to the official reference rat genome (rn5).

So how can one solve this isse?
-Is there a way to import a proper genome for use with Tophat2? Ideally directly indo Galaxy without prior download.
-If not, how does Tophat2 differ from "Tophat for Illumina". Can one also analyze non-Illumina data with that? As I understand it Tophat2 is faster than the previous version?

Thanks in advance for any help.