References

1: Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, and et al. Sustainable data analysis with snakemake. F1000Research, 10:33, Apr 2021. URL: http://dx.doi.org/10.12688/f1000research.29032.2, doi:10.12688/f1000research.29032.2. 2: R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2021. URL: https://www.R-project.org/. 3: Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, and Vincent J. Carey. Software for computing and annotating genomic ranges. PLoS Computational Biology, 9(8):e1003118, Aug 2013. URL: http://dx.doi.org/10.1371/journal.pcbi.1003118, doi:10.1371/journal.pcbi.1003118. 4: M. Lawrence, R. Gentleman, and V. Carey. Rtracklayer: an r package for interfacing with genome browsers. Bioinformatics, 25(14):1841–1842, May 2009. URL: http://dx.doi.org/10.1093/bioinformatics/btp328, doi:10.1093/bioinformatics/btp328. 5: Hadley Wickham, Mara Averick, Jennifer Bryan, Winston Chang, Lucy McGowan, Romain François, Garrett Grolemund, Alex Hayes, Lionel Henry, Jim Hester, and et al. Welcome to the tidyverse. Journal of Open Source Software, 4(43):1686, Nov 2019. URL: http://dx.doi.org/10.21105/joss.01686, doi:10.21105/joss.01686. 6: Liguo Wang, Shengqin Wang, and Wei Li. RSeQC: quality control of RNA-seq experiments. Bioinformatics, 28(16):2184–2185, June 2012. URL: https://doi.org/10.1093/bioinformatics/bts356, doi:10.1093/bioinformatics/bts356. 7: Simon Andrews, Felix Krueger, Anne Segonds-Pichon, Laura Biggins, Christel Krueger, and Steven Wingett. FastQC. Babraham Institute, January 2012. URL: https://qubeshub.org/resources/fastqc. 8: Philip Ewels, Måns Magnusson, Sverker Lundin, and Max Käller. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19):3047–3048, Jun 2016. URL: http://dx.doi.org/10.1093/bioinformatics/btw354, doi:10.1093/bioinformatics/btw354. 9: Shihao Shen, Juw Won Park, Zhi-xiang Lu, Lan Lin, Michael D. Henry, Ying Nian Wu, Qing Zhou, and Yi Xing. Rmats: robust and flexible detection of differential alternative splicing from replicate rna-seq data. Proceedings of the National Academy of Sciences, 111(51):E5593–E5601, Dec 2014. URL: http://dx.doi.org/10.1073/pnas.1419161111, doi:10.1073/pnas.1419161111. 10: Stephen W. Hartley and James C. Mullikin. Detection and visualization of differential splicing in RNA-seq data with JunctionSeq. Nucleic Acids Research, pages gkw501, June 2016. URL: https://doi.org/10.1093/nar/gkw501, doi:10.1093/nar/gkw501. 11: Jorge Vaquero-Garcia, Alejandro Barrera, Matthew R Gazzara, Juan Gonzalez-Vallinas, Nicholas F Lahens, John B Hogenesch, Kristen W Lynch, and Yoseph Barash. A new view of transcriptome complexity and regulation through the lens of local splicing variations. eLife, February 2016. URL: https://doi.org/10.7554/elife.11752, doi:10.7554/elife.11752. 12: Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, and Jonathan K. Pritchard. Annotation-free quantification of RNA splicing using LeafCutter. Nature Genetics, 50(1):151–158, December 2017. URL: https://doi.org/10.1038/s41588-017-0004-9, doi:10.1038/s41588-017-0004-9. 13: Sam Kovaka, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, and Mihaela Pertea. Transcriptome assembly from long-read rna-seq alignments with stringtie2. Genome Biology, Dec 2019. URL: http://dx.doi.org/10.1186/s13059-019-1910-1, doi:10.1186/s13059-019-1910-1. 14: Jennifer V Gerbracht, Volker Boehm, Thiago Britto-Borges, Sebastian Kallabis, Janica L Wiederstein, Simona Ciriello, Dominik U Aschemeier, Marcus Krüger, Christian K Frese, Janine Altmüller, and et al. Casc3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex. Nucleic Acids Research, 48(15):8626–8644, Jul 2020. URL: http://dx.doi.org/10.1093/nar/gkaa564, doi:10.1093/nar/gkaa564.