Zhou, AoBreese, Marcus R.Hao, YangyangEdenberg, Howard J.Li, LangSkaar, Todd C.Liu, Yunlong2022-10-102022-10-102012Zhou, A., Breese, M. R., Hao, Y., Edenberg, H. J., Li, L., Skaar, T. C., & Liu, Y. (2012). Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data. BMC Genomics, 13 Suppl 8(Suppl 8), S10. https://doi.org/10.1186/1471-2164-13-S8-S10https://hdl.handle.net/1805/30303BACKGROUND: Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing. RESULTS: We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure. CONCLUSIONS: Alt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.enAttribution 4.0 InternationalAlgorithmsAlternative SplicingRNA Sequence AnalysisSequencing DepthAlcohol ExposureCassette ExonArticle