As everything you can't really let the tools run on autopilot without knowing what it is you're doing or why. My suggestion would be read the documentation and actually get a feel about what each parameter does.
If you're pushed for time to get some results or need to confirm a hypothesis you have I would suggest using HISAT2 on galaxy. It's far less fiddly with less things to play around with and much faster. You can then do your analysis downstream using DEseq2.
TopHat might take abit longer to optimise but ideally should give you more or less the same results at the end.
Hope that helps,
2.2 years ago by
VY • 120