I would like to get DEG for my RNAseq. I have completed these steps: cufflinks, and cuffdiff. But when I am trying to run CummeRbund in the galaxy by using SQLite files output of cuffdiff as the input for CummeRbund, I get this error every time: The tool was executed with one or more empty input datasets. This frequently results in tool errors due to problematic input choices. I would appreciate it if you could guide me on how to fix it. How should I use CummeRbund in the galaxy?
And are there other alternative tools to get DEG from FPKM data in the galaxy?
Thank you very much