Dear all, newbie question here.
So I installed Galaxy on my linux box. When I try to upload a dataset I see a drop down for reference genome; I chose this and was able to upload successfully. However, when I tried to use a tool that I installed, TopHat Illumina, the place where the choose reference genome does not contain any of the genome listed in the upload section. Its just an empty box. Question I have is how do I install a reference genome (ie mouse mm9) so that I can get it to work with TopHat. I'm a bit confused since it was present in the upload section but not here, so maybe I don't need to install the reference genome?
thank you very much!