Welcome, @platonm
Does this prior answer address the problem? Issue with StringTie Output File when using DESeq2 option - #5 by jennaj
And, you might need to double check your reference data. It seems that either the GTF isn’t a match for the reference genome, or, more likely, there is some format problem (headers?). This guide has more details about what to check when using these tools → FAQ: Extended Help for Differential Expression Analysis Tools
Please give those a review and let us know if you solve this. For more troubleshooting here, we’ll need to see what you have so far. The banner at this forum has instructions, or see here directly:
- Troubleshooting resources for errors or unexpected results
- How to get faster help with your question
Let’s start here! 