I am trying to map RNA-seq reads to a GFF annotation file I created using tophat2 through Galaxy. When trying to select a reference genome from my history files, no file is identified as an option. I've uploaded a GFF3 file. the same thing happened even when I've uploaded a GTF file from the "RNA-seq Analysis Exercise" page (named Galaxy Dataset | iGenomes UCSC hg19, chr19 gene annotation).
What am I doing wrong and how can I get tophat to work with my data?