Error in CummeRbund


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


Hello @MMM

The error means that the database wasn’t created correctly. The tool suite you are using is known to have issues. Using updated protocols is recommended.

Please see the Galaxy tutorials here. If you run into problems, this forum has much Q&A around troubleshooting: search by tool name or datatype.


Thank you for your reply.