edgeR troubleshooting

Can someone please help me run edgeR on galaxy? I got output files with kallisto and even had only 2 columns and whatever I do edgeR keeps failing. The reads are single end. I have not tried using a single count matrix, but shouldn’t it work with individual files? What do I do to get the single files to work? I did upload 2 files for each level.

Welcome, @User123456790

This guide helps to solve most usage errors with Bioconductor tools → FAQ: Extended Help for Differential Expression Analysis Tools

Please give that a review, make adjustments as needed, then try a rerun.

For any outstanding problems, you can post back more details about your work and we can try to help more. See the banner at this forum, or directly at these resources for the how to share data in Galaxy. You can post your data links or screenshot back here.

About this part:

By the point where you are running edgeR, you will be using tabular count files and a tabular mapping file or GTF reference. So focusing on those parts of your data will likely spot the problem. You may still need to back up and re-do some steps but you’ll be able to determine what is needed from these files alone.

Let’s start there :slight_smile: