Hi @julsies
Try running your GTF annotation through the Stringtie merge tool first (by itself) to adjust formatting. Then, run the Stringtie merge tool again with all of your Stringtie outputs along with the modified GTF.
Prior Q&A with more details:
Why is this needed? The tool expects a slightly modified version of GTF format. The annotation file included with the tutorial is already adjusted, so that step wasn’t included. Avoid GFF3 formatted annotation with this tool and most others, unless specifically noted otherwise on a tool form. More details are in the topic above, and those usually help to solve troubleshooting issues with this tool.
One last potential format issue to check for: A common item to correct as a data cleaning/prep step (any analysis/tool) is to remove GTF headers. Strict GTF format does not include headers, only data lines, but some data providers include one or more anyway for practical reasons (versioning, etc). So, if headers are present in your file, usually at the top and starting with a #, remove those first before using the annotation in any analysis steps. (Note: GFF3 format will have at least one header line, but that is in the specification for the datatype).
If all that still fails, then more is going on and @gallardoalba can help with the history review 