{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T19:22:32Z","timestamp":1776453752988,"version":"3.51.2"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed.<\/jats:p>\n               <jats:p>Results: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM\/SAM files containing hundreds of millions of alignments.<\/jats:p>\n               <jats:p>Availability and implementation: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http:\/\/code.google.com\/p\/rseqc\/.<\/jats:p>\n               <jats:p>Contact: \u00a0WL1@bcm.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts356","type":"journal-article","created":{"date-parts":[[2012,6,29]],"date-time":"2012-06-29T00:52:19Z","timestamp":1340931139000},"page":"2184-2185","source":"Crossref","is-referenced-by-count":2543,"title":["RSeQC: quality control of RNA-seq experiments"],"prefix":"10.1093","volume":"28","author":[{"given":"Liguo","family":"Wang","sequence":"first","affiliation":[{"name":"1 Division of Biostatistics, Dan L. Duncan Cancer Center and 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and 3State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"},{"name":"1 Division of Biostatistics, Dan L. Duncan Cancer Center and 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and 3State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}]},{"given":"Shengqin","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Division of Biostatistics, Dan L. Duncan Cancer Center and 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and 3State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}]},{"given":"Wei","family":"Li","sequence":"additional","affiliation":[{"name":"1 Division of Biostatistics, Dan L. Duncan Cancer Center and 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and 3State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"},{"name":"1 Division of Biostatistics, Dan L. Duncan Cancer Center and 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and 3State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}]}],"member":"286","published-online":{"date-parts":[[2012,6,27]]},"reference":[{"key":"2023012512530946200_B1","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012512530946200_B2","first-page":"1530","article-title":"RNA-SeQC: RNA-seq metrics for quality control and process optimization","volume":"28","author":"Deluca","year":"2012","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012512530946200_B3","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol."},{"key":"2023012512530946200_B4","doi-asserted-by":"crossref","first-page":"e131","DOI":"10.1093\/nar\/gkq224","article-title":"Biases in Illumina transcriptome sequencing caused by random hexamer priming","volume":"38","author":"Hansen","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512530946200_B5","first-page":"130","article-title":"SAMStat: monitoring biases in next generation sequencing data","volume":"27","author":"Lassmann","year":"2011","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012512530946200_B6","first-page":"589","article-title":"htSeqTools: high-throughput sequencing quality control, processing and visualization in R","volume":"28","author":"Planet","year":"2012","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012512530946200_B7","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"GenePattern 2.0","volume":"38","author":"Reich","year":"2006","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2184\/48870333\/bioinformatics_28_16_2184.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2184\/48870333\/bioinformatics_28_16_2184.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:50:50Z","timestamp":1674669050000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/16\/2184\/325191"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,27]]},"references-count":7,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2012,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts356","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,8,15]]},"published":{"date-parts":[[2012,6,27]]}}}