Users can potentially use any annotation file with tappAS. However, it is required that users functionally annotate the file and re-format it as a tappAS-compatible GFF3. Since this is not a trivial task, we currently provide pre-annotated reference GFF3 files for ENSEMBL and RefSeq for mouse, human and a few other model organisms, but only for some versions of the annotation. We recommend checking the tappAS paper for further information on transcriptome versions and the functional label categories they contain.