TappAS s a GFF3-like format for its transcriptome annotation, but it is not exactly the same as just providing a GFF3 file for the transcriptome used for isoform quantification.
When we refer to tappAS annotation file, we are referring to not only traditional transcript annotation, but also to functional annotation. This means that our GFF3 files are formatted to combine both traditional annotation features (transcripts, exons, etc.) and functional labels, including, but not limited to, UTR lengths, CDS positions, predicted PFAM domains, sequence motifs, etc. More details about annotated functional categories and their source databases are available in our tappAS paper. Details about this GFF3-based formatting can be found in the “Projects” section of our website’s Overview page.