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As RNA-seq has become a routine protocol for transcriptome analysis, it is of great interest to leverage such unprecedented collection of RNA-seq data by new computational methods to extract and quantify APA dynamics in these transcriptomes. However, research progress in this area has been relatively limited. Conventional methods rely on either transcript assembly to determine transcript 3\u2032 ends or annotated poly(A) sites. Moreover, they can neither identify more than two poly(A) sites in a gene nor detect dynamic APA site usage considering more than two poly(A) sites.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed an approach called APAtrap based on the mean squared error model to identify and quantify APA sites from RNA-seq data. APAtrap is capable of identifying novel 3\u2032 UTRs and 3\u2032 UTR extensions, which contributes to locating potential poly(A) sites in previously overlooked regions and improving genome annotations. APAtrap also aims to tally all potential poly(A) sites and detect genes with differential APA site usages between conditions. Extensive comparisons of APAtrap with two other latest methods, ChangePoint and DaPars, using various RNA-seq datasets from simulation studies, human and Arabidopsis demonstrate the efficacy and flexibility of APAtrap for any organisms with an annotated genome.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Freely available for download at https:\/\/apatrap.sourceforge.io.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty029","type":"journal-article","created":{"date-parts":[[2018,1,17]],"date-time":"2018-01-17T12:19:00Z","timestamp":1516191540000},"page":"1841-1849","source":"Crossref","is-referenced-by-count":109,"title":["APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data"],"prefix":"10.1093","volume":"34","author":[{"given":"Congting","family":"Ye","sequence":"first","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China"}]},{"given":"Yuqi","family":"Long","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University, Xiamen, Fujian, China"}]},{"given":"Guoli","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University, Xiamen, Fujian, China"}]},{"given":"Qingshun Quinn","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China"},{"name":"Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA"}]},{"given":"Xiaohui","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University, Xiamen, Fujian, China"}]}],"member":"286","published-online":{"date-parts":[[2018,1,18]]},"reference":[{"key":"2023012810011726700_bty029-B1","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1080\/15476286.2015.1040974","article-title":"Global insights into alternative polyadenylation regulation","volume":"12","author":"Batra","year":"2015","journal-title":"RNA Biol"},{"key":"2023012810011726700_bty029-B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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