Fig. 1

Overview tappAS usage. a tappAS project creation workflow. tappAS requires three input files: a transcript-level expression matrix, an experimental design file, and a transcript-level functional annotation file. The expression matrix is typically obtained by mapping RNA-Seq short reads to either a reference transcriptome, a user-defined transcriptome, or an experiment-specific, full-length transcriptome obtained by long-read sequencing. In the last two last cases, the functional annotation file needs to be created using the IsoAnnot_Lite script and provided as input upon project creation. When the reference transcriptome is used, users may select tappAS built-in annotation files. b The main features of tappAS graphical user interface (GUI)