I’m having trouble running EdgeR after running StringTie. The error I get when I try to run is that the gene counts are differing in numbers. Prior to the update for Galaxy, we had no issues in running these samples, but now we’re unsure where the issues coming from.
How do we make it that when running the samples the gene counts numbers are the same? I ran StringTie with “User reference transcripts only” parameter as “Yes”, but the issue still stays.
Welcome, @simeix
In general, we recommend using Featurecounts or HTseq-count instead for the counting step. An example of this usage can be found in a few of our tutorials.
That said, we have other reports of the newer Stringtie behaving differently, and that might be a problem, but I don’t have a concrete example yet. If you want to share your work I’m willing to take a closer look. Please see → How to get faster help with your question. I would need the shared history with everything in context for bug hunting.
Another solution could be to just keep using the version of the tool that already works for you.
So … whether the change is a Galaxy change (and maybe bug we can fix) or a change in the underlying tool itself (we can’t change that, only the Bioconductor team can do that) is not clear. And, we’d be interested in correcting anything that is possible on our side.
Let’s start there, thanks and hopefully we can follow up and solve this! 
