[galaxy-user] RNA seq analysis

Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for "maximum number of alignments to be allowed" is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP