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Robust ASE analysis requires the integration of multiple computational steps, including read alignment, read counting, data visualization, and statistical testing\u2014this complexity creates challenges for reproducibility, scalability, and ease of use. Here, we present ASE Toolkit (ASET), an end-to-end pipeline that streamlines SNP-level ASE data generation, visualization, and testing for parent-of-origin (PofO) effect. ASET includes a modular pipeline built with Nextflow for ASE quantification from short-read transcriptome sequencing reads, an R library for data visualization, and a Julia script for PofO testing. ASET performs comprehensive read quality control, SNP-tolerant alignment to reference genomes, read counting with allele and strand resolution, annotation with genes and exons, and estimation of contamination. In sum, ASET provides a complete and easy-to-use solution for molecular and biomedical scientists to identify and interpret patterns of ASE from RNA-Seq data.<\/jats:p>","DOI":"10.1186\/s12859-025-06282-2","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T10:24:30Z","timestamp":1761042270000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["ASET: an end-to-end pipeline for quantification and visualization of allele specific expression"],"prefix":"10.1186","volume":"26","author":[{"given":"Weisheng","family":"Wu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerby","family":"Shedden","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudius","family":"Vincenz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Gates","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beverly","family":"Strassmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"issue":"7","key":"6282_CR1","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1101\/GR.192278.115","volume":"25","author":"Y Baran","year":"2015","unstructured":"Baran Y, et al. \u2018The landscape of genomic imprinting across diverse adult human tissues.\u2019 Genome Res. 2015;25(7):927\u201336. https:\/\/doi.org\/10.1101\/GR.192278.115.","journal-title":"Genome Res"},{"key":"6282_CR2","doi-asserted-by":"publisher","DOI":"10.1038\/NATURE24277","author":"F Aguet","year":"2017","unstructured":"Aguet F, et al. Genetic effects on gene expression across human tissues. Nature. 2017. https:\/\/doi.org\/10.1038\/NATURE24277.","journal-title":"Nature"},{"issue":"7468","key":"6282_CR3","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/NATURE12531","volume":"501","author":"T Lappalainen","year":"2013","unstructured":"Lappalainen T, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501(7468):506\u201311. https:\/\/doi.org\/10.1038\/NATURE12531.","journal-title":"Nature"},{"issue":"7440","key":"6282_CR4","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/NATURE11968","volume":"495","author":"RJ Schmitz","year":"2013","unstructured":"Schmitz RJ, et al. Patterns of population epigenomic diversity. 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Bioinformatics. 2009;25(24):3207\u201312. https:\/\/doi.org\/10.1093\/BIOINFORMATICS\/BTP579.","journal-title":"Bioinformatics"},{"key":"6282_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/MSB.2011.54","author":"J Rozowsky","year":"2011","unstructured":"Rozowsky J, et al. \u2018AlleleSeq: analysis of allele-specific expression and binding in a network framework.\u2019 Mol Syst Biol. 2011. https:\/\/doi.org\/10.1038\/MSB.2011.54.","journal-title":"Mol Syst Biol"},{"key":"6282_CR9","doi-asserted-by":"publisher","DOI":"10.12688\/F1000RESEARCH.9037.2","author":"F Krueger","year":"2016","unstructured":"Krueger F, Andrews SR. \u2018SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes.\u2019 F1000Res. 2016. https:\/\/doi.org\/10.12688\/F1000RESEARCH.9037.2.","journal-title":"F1000Res"},{"key":"6282_CR10","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-3578-9_15","author":"TD Wu","year":"2016","unstructured":"Wu TD, et al. 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The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"257"}}