Hi @SRFlin
The tool is reporting that it found transcripts that were not found in the BAM. The identifiers are not simplfied, and I’m not sure which GTF that is (Gencode for both?).
I have a history here where I re-downloaded the UCSC files since I always forget which are the paired files, plus wanted to make sure something didn’t change. The built-in hg38 index would be an appropriate choice to use with the tagged data in here, and it sounds like that is what you used.
You can just review, or import this and use the data. https://usegalaxy.org/u/jen-galaxyproject/h/ucsc-hg38-gtfs-mrna
I’d be curious about how that works out. It might be time to share your history if this doesn’t work – include the run that uses those files if possible since I know those should work.