2.6 years ago by
Including reference annotation can help (to make sure that known splices are captured). This option is under TopHat settings to use: Full parameters: Do you want to supply your own junction data? Yes. There are a few ways to set this, maybe try a few to see which works best with your data/goals and decide.
For hg38, iGenomes has a reference GTF that would be a good choice to use, for this tool and others downstream in the Tuxedo RNA-seq analysis pathway. Download the hg38 tar file, unpack it, then load just the genes.gtf file up into Galaxy for use.
Others can offer more help if they want.
Best, Jen, Galaxy team