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. 2020 May 18;21:119. doi: 10.1186/s13059-020-02028-w

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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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)