Alternative splicing (AS) is a regulatory process during mRNA maturation that shapes higher eukaryotes’ complex transcriptomes. High-throughput sequencing of RNA (RNA-Seq) allows for measurements of AS transcripts at an unprecedented depth and diversity. The ever-expanding catalog of known AS events provides biological insights into gene regulation, population genetics, or in the context of disease. Here, we present an overview on the usage of SplAdder, a graph-based alternative splicing toolbox, which can integrate an arbitrarily large number of RNA-Seq alignments and a given annotation file to augment the shared annotation based on RNA-Seq evidence. The shared augmented annotation graph is then used to identify, quantify, and confirm alternative splicing events based on the RNA-Seq data. Splice graphs for individual alignments can also be tested for significant quantitative differences between other samples or groups of samples.
CITATION STYLE
Markolin, P., Rätsch, G., & Kahles, A. (2022). Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder. In Methods in Molecular Biology (Vol. 2493, pp. 167–193). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2293-3_11
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