If you want to use your own version of the transcriptome instead of one of tappAS’ available annotation versions, the only current way around this is to use our IsoAnnotLite tool to transfer functional labels from our GFF3 files to your own GTF annotation file. This will create a GFF3 file that is compatible with tappAS and that contains at least part of our reference transcriptome’s functional labels.
However, this process is done based on genomic positions, and therefore some functional annotations may be lost in the process and/or some transcripts may remain unnanoted because they were not in the transcriptome version that we’re using. More information on how to use IsoAnnotLite with any annotation file can be found here. Of note, you will require SQANTI3 output files to use IsoAnnotLite, but the tool can also be run jointly with SQANTI3 via the the –isoAnnotLite argument (see SQANTI3 README for details).