I am attempting to analyse my first RNA-seq experiment using Tuxedo tools. When I attempt to cuffmerge my assembled transcripts from cufflinks I get an error "Fatal error: Matched on Error Error running cuffmerge." and looking at the issue it says: "ValueError: invalid literal for int() with base 10: " I have attempted using older versions of cuffmerge 0.0.6 and rerunning cufflinks. I am pretty stuck with little experience on the platform. Any help would be much appreciated.
I see the bug report you sent in about the same problem.
This error occurs when the Custom reference genome is malformed or when there is a reference genome mixup. All inputs and database assignments must be from the exact same genome build.
Here is how to double check your inputs:
Thanks, Jen, Galaxy team