I've been trying to use Tophat for the past week but I keep encountering an issue where the run appears to begin (turns yellow) and runs for a few hours but then reverts back to gray and says waiting to run (no error message).
After maybe 8 tries one of my samples worked but the other one still has this issue. I've tried reuploading the fastqsanger files and retrying but it doesn't appear to help.
Could someone tell me what is going on with Tophat? Does each Tophat run need to enter the queue twice or something?