{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T22:37:44Z","timestamp":1775601464734,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,3,2]],"date-time":"2021-03-02T00:00:00Z","timestamp":1614643200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HHSN268201000029C"],"award-info":[{"award-number":["HHSN268201000029C"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Broad Institute, Inc"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Post-sequencing quality control is a crucial component of RNA sequencing (RNA-seq) data generation and analysis, as sample quality can be affected by sample storage, extraction and sequencing protocols. RNA-seq is increasingly applied to cohorts ranging from hundreds to tens of thousands of samples in size, but existing tools do not readily scale to these sizes, and were not designed for a wide range of sample types and qualities. Here, we describe RNA-SeQC 2, an efficient reimplementation of RNA-SeQC (DeLuca et al., 2012) that adds multiple metrics designed to characterize sample quality across a wide range of RNA-seq protocols.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The command-line tool, documentation and C++ source code are available at the GitHub repository https:\/\/github.com\/getzlab\/rnaseqc. Code and data for reproducing the figures in this paper are available at https:\/\/github.com\/getzlab\/rnaseqc2-paper.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab135","type":"journal-article","created":{"date-parts":[[2021,2,27]],"date-time":"2021-02-27T04:10:21Z","timestamp":1614399021000},"page":"3048-3050","source":"Crossref","is-referenced-by-count":117,"title":["RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts"],"prefix":"10.1093","volume":"37","author":[{"given":"Aaron","family":"Graubert","sequence":"first","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9414-300X","authenticated-orcid":false,"given":"Fran\u00e7ois","family":"Aguet","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"given":"Arvind","family":"Ravi","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"given":"Kristin G","family":"Ardlie","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0936-0753","authenticated-orcid":false,"given":"Gad","family":"Getz","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"Cancer Center and Department of Pathology, Massachusetts General Hospital , Boston, MA 02114, USA"},{"name":"Department of Pathology, Harvard Medical School , Boston, MA 02115, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,3,2]]},"reference":[{"key":"2023061310541316400_btab135-B1","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/bioinformatics\/bts196","article-title":"RNA-SeQC: RNA-seq metrics for quality control and process optimization","volume":"28","author":"DeLuca","year":"2012","journal-title":"Bioinformatics"},{"key":"2023061310541316400_btab135-B2","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2023061310541316400_btab135-B3","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.cell.2020.06.013","article-title":"Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma","volume":"182","author":"Gillette","year":"2020","journal-title":"Cell"},{"key":"2023061310541316400_btab135-B4","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.aaz1776","article-title":"The GTEx Consortium atlas of genetic regulatory effects across human tissues","volume":"369","year":"2020","journal-title":"Science"},{"key":"2023061310541316400_btab135-B5","doi-asserted-by":"crossref","first-page":"eaaz8528","DOI":"10.1126\/science.aaz8528","article-title":"Cell type-specific genetic regulation of gene expression across human tissues","volume":"369","author":"Kim-Hellmuth","year":"2020","journal-title":"Science"},{"key":"2023061310541316400_btab135-B6","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061310541316400_btab135-B7","doi-asserted-by":"crossref","first-page":"e1000770","DOI":"10.1371\/journal.pcbi.1000770","article-title":"A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies","volume":"6","author":"Stegle","year":"2010","journal-title":"PLoS Comput. 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