{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T22:46:53Z","timestamp":1785192413681,"version":"3.55.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Discovery of novel splicing from RNA sequence data remains a critical and exciting focus of transcriptomics, but reduced alignment power impedes expression quantification of novel splice junctions.<\/jats:p>\n               <jats:p>Results: Here, we profile performance characteristics of two-pass alignment, which separates splice junction discovery from quantification. Per sample, across a variety of transcriptome sequencing datasets, two-pass alignment improved quantification of at least 94% of simulated novel splice junctions, and provided as much as 1.7-fold deeper median read depth over those splice junctions. We further demonstrate that two-pass alignment works by increasing alignment of reads to splice junctions by short lengths, and that potential alignment errors are readily identifiable by simple classification. Taken together, two-pass alignment promises to advance quantification and discovery of novel splicing events.<\/jats:p>\n               <jats:p>Contact: \u00a0arul@med.umich.edu, nesvi@med.umich.edu<\/jats:p>\n               <jats:p>Availability and implementation: Two-pass alignment was implemented here as sequential alignment, genome indexing, and re-alignment steps with STAR. Full parameters are provided in Supplementary Table 2.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv642","type":"journal-article","created":{"date-parts":[[2015,10,31]],"date-time":"2015-10-31T02:38:11Z","timestamp":1446259091000},"page":"43-49","source":"Crossref","is-referenced-by-count":73,"title":["Two-pass alignment improves novel splice junction quantification"],"prefix":"10.1093","volume":"32","author":[{"given":"Brendan A.","family":"Veeneman","sequence":"first","affiliation":[{"name":"1 Department of Computational Medicine and Bioinformatics,"},{"name":"2 Michigan Center for Translational Pathology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudhanshu","family":"Shukla","sequence":"additional","affiliation":[{"name":"2 Michigan Center for Translational Pathology,"},{"name":"3 Department of Pathology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saravana M.","family":"Dhanasekaran","sequence":"additional","affiliation":[{"name":"2 Michigan Center for Translational Pathology,"},{"name":"3 Department of Pathology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arul M.","family":"Chinnaiyan","sequence":"additional","affiliation":[{"name":"1 Department of Computational Medicine and Bioinformatics,"},{"name":"2 Michigan Center for Translational Pathology,"},{"name":"3 Department of Pathology,"},{"name":"4 Department of Urology and"},{"name":"5 Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey I.","family":"Nesvizhskii","sequence":"additional","affiliation":[{"name":"1 Department of Computational Medicine and Bioinformatics,"},{"name":"2 Michigan Center for Translational Pathology,"},{"name":"3 Department of Pathology,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,10,30]]},"reference":[{"key":"2023020110220516900_btv642-B1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2023020110220516900_btv642-B2","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature11233","article-title":"Landscape of transcription in human cells","volume":"489","author":"Djebali","year":"2012","journal-title":"Nature"},{"key":"2023020110220516900_btv642-B3","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020110220516900_btv642-B4","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nmeth.2722","article-title":"Systematic evaluation of spliced alignment programs for RNA-seq data","volume":"10","author":"Engstrom","year":"2013","journal-title":"Nat. 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