I am conducting an RNA-seq analysis with Saccharomyces cerevisiae-derived data. In my workflow, I am using the 'TopHat accepted hits' BAM output files as input for a downstream Cufflinks analysis on the main Galaxy server online. All of my Cufflinks outputs, however, are coming out blank(i.e nothing in the skipped, or assembled transcript files, or the transcript/gene expression files)! Curiously, when I do a reference-free analysis, I get an output; however, it isn't very useful for an RNA-seq analysis. To me, this suggests that the BAM files are OK, and that there is some issue with the reference annotation GFF file. However, I have previously used the same GFF file successfully for a similar analysis. The said GFF file was downloaded from the Saccharomyces Genome Database, wherein the only change I made was to keep just the annotations and remove the FASTA sequence for all the chromosomes.