The best way to use tappAS is to generate one transcriptome for all sequenced samples. To do this, users should pre-process all SMRT cells together using IsoSeq3, and then run SQANTI3 on the output of this joint run. IsoSeq3 documentation contains more info on how to merge SMRT cells -typically all users will need to do is merge the output of the refine command, and then repeat the clustering step. See the IsoSeq3 documentation IsoSeq3 documentation for details.
WARNING: note that the QC report produced by SQANTI3 can help you make informed decisions about isoforms that might be false positives or low quality, and we strongly advise you to remove them from your transcriptome before you continue your analysis. We recommend reading the SQANTI paper to get a better idea of how to produce a high-quality, curated transcriptome.