I am new to Galaxy, and for my first project I wish to analyze some sequences we recently obtained from an RNA-Seq experiment. I am stuck at the step of using TopHat/Bowtie for aligning my FASTQ files to a S.cerevisiae reference genome (preferably, S288C). The problem is that I don't see any S.cerevisiae reference genome from the list of built-in reference genomes. This is confusing, because Galaxy clearly has this sequence on its server (the genome option appears in the Get Data-->Upload file menu at the bottom right-hand corner, for example). Could you comment on this?
Anyway, I am currently trying to use the alternate option of manually uploading a reference genome to my history and using that as a reference for my analyses but even this isn't nearly as straightforward as I thought, probably because I have a Windows machine. Is there a source from where I can download an annotated S288C genome as a FASTA file as a single file? I downloaded S288C_reference_genome_R64-2-1_20150113.tgz but I only see Chromosome 1 in this file.