ERROR: no features were loaded in GTF format. The annotation format can be specified by the ‘-F’ option, and the required feature type can be specified by the ‘-t’ option..
Does this mean that there are no features annotated in my reference GTF file?
So far, I have checked my annotated transcript when I run GffCompare anf it is empty while the output off Stringtie merge have data, I don’t why
It sounds like you have Featurecounts configured to look for a feature type that does not exist in your GTF file (3rd column of the reference annotation file is searched with the term set on the tool form). Related Q&A → Problems with the tool featureCounts: Fatal error: Exit code 255 ()
The tutorial data should be consistent with the steps in the tutorial, but if you are using your own reference data instead, you may need to make small adjustments.
For the other problem (an empty file?), it is hard to guess without seeing the data. Are you saying that the upstream Gffcompare step produced an empty result? If you want to generate a share link back to the history and post it into a reply, we can help to troubleshoot what is going wrong.
