Aaron Graubert1, François Aguet1, Arvind Ravi1, Kristin G Ardlie1, Gad Getz1,2,3. 1. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. 2. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. 3. Harvard Medical School, Boston, MA 02115, USA.
Abstract
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The command-line tool, documentation, and C ++ source code are available at the GitHub repository https://github.com/getzlab/rnaseqc. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The command-line tool, documentation, and C ++ source code are available at the GitHub repository https://github.com/getzlab/rnaseqc. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Authors: Sarah Kim-Hellmuth; François Aguet; Meritxell Oliva; Manuel Muñoz-Aguirre; Silva Kasela; Valentin Wucher; Stephane E Castel; Andrew R Hamel; Ana Viñuela; Amy L Roberts; Serghei Mangul; Xiaoquan Wen; Gao Wang; Alvaro N Barbeira; Diego Garrido-Martín; Brian B Nadel; Yuxin Zou; Rodrigo Bonazzola; Jie Quan; Andrew Brown; Angel Martinez-Perez; José Manuel Soria; Gad Getz; Emmanouil T Dermitzakis; Kerrin S Small; Matthew Stephens; Hualin S Xi; Hae Kyung Im; Roderic Guigó; Ayellet V Segrè; Barbara E Stranger; Kristin G Ardlie; Tuuli Lappalainen Journal: Science Date: 2020-09-11 Impact factor: 63.714
Authors: Daniel Taliun; Daniel N Harris; Michael D Kessler; Jedidiah Carlson; Zachary A Szpiech; Raul Torres; Sarah A Gagliano Taliun; André Corvelo; Stephanie M Gogarten; Hyun Min Kang; Achilleas N Pitsillides; Jonathon LeFaive; Seung-Been Lee; Xiaowen Tian; Brian L Browning; Sayantan Das; Anne-Katrin Emde; Wayne E Clarke; Douglas P Loesch; Amol C Shetty; Thomas W Blackwell; Albert V Smith; Quenna Wong; Xiaoming Liu; Matthew P Conomos; Dean M Bobo; François Aguet; Christine Albert; Alvaro Alonso; Kristin G Ardlie; Dan E Arking; Stella Aslibekyan; Paul L Auer; John Barnard; R Graham Barr; Lucas Barwick; Lewis C Becker; Rebecca L Beer; Emelia J Benjamin; Lawrence F Bielak; John Blangero; Michael Boehnke; Donald W Bowden; Jennifer A Brody; Esteban G Burchard; Brian E Cade; James F Casella; Brandon Chalazan; Daniel I Chasman; Yii-Der Ida Chen; Michael H Cho; Seung Hoan Choi; Mina K Chung; Clary B Clish; Adolfo Correa; Joanne E Curran; Brian Custer; Dawood Darbar; Michelle Daya; Mariza de Andrade; Dawn L DeMeo; Susan K Dutcher; Patrick T Ellinor; Leslie S Emery; Celeste Eng; Diane Fatkin; Tasha Fingerlin; Lukas Forer; Myriam Fornage; Nora Franceschini; Christian Fuchsberger; Stephanie M Fullerton; Soren Germer; Mark T Gladwin; Daniel J Gottlieb; Xiuqing Guo; Michael E Hall; Jiang He; Nancy L Heard-Costa; Susan R Heckbert; Marguerite R Irvin; Jill M Johnsen; Andrew D Johnson; Robert Kaplan; Sharon L R Kardia; Tanika Kelly; Shannon Kelly; Eimear E Kenny; Douglas P Kiel; Robert Klemmer; Barbara A Konkle; Charles Kooperberg; Anna Köttgen; Leslie A Lange; Jessica Lasky-Su; Daniel Levy; Xihong Lin; Keng-Han Lin; Chunyu Liu; Ruth J F Loos; Lori Garman; Robert Gerszten; Steven A Lubitz; Kathryn L Lunetta; Angel C Y Mak; Ani Manichaikul; Alisa K Manning; Rasika A Mathias; David D McManus; Stephen T McGarvey; James B Meigs; Deborah A Meyers; Julie L Mikulla; Mollie A Minear; Braxton D Mitchell; Sanghamitra Mohanty; May E Montasser; Courtney Montgomery; Alanna C Morrison; Joanne M Murabito; Andrea Natale; Pradeep Natarajan; Sarah C Nelson; Kari E North; Jeffrey R O'Connell; Nicholette D Palmer; Nathan Pankratz; Gina M Peloso; Patricia A Peyser; Jacob Pleiness; Wendy S Post; Bruce M Psaty; D C Rao; Susan Redline; Alexander P Reiner; Dan Roden; Jerome I Rotter; Ingo Ruczinski; Chloé Sarnowski; Sebastian Schoenherr; David A Schwartz; Jeong-Sun Seo; Sudha Seshadri; Vivien A Sheehan; Wayne H Sheu; M Benjamin Shoemaker; Nicholas L Smith; Jennifer A Smith; Nona Sotoodehnia; Adrienne M Stilp; Weihong Tang; Kent D Taylor; Marilyn Telen; Timothy A Thornton; Russell P Tracy; David J Van Den Berg; Ramachandran S Vasan; Karine A Viaud-Martinez; Scott Vrieze; Daniel E Weeks; Bruce S Weir; Scott T Weiss; Lu-Chen Weng; Cristen J Willer; Yingze Zhang; Xutong Zhao; Donna K Arnett; Allison E Ashley-Koch; Kathleen C Barnes; Eric Boerwinkle; Stacey Gabriel; Richard Gibbs; Kenneth M Rice; Stephen S Rich; Edwin K Silverman; Pankaj Qasba; Weiniu Gan; George J Papanicolaou; Deborah A Nickerson; Sharon R Browning; Michael C Zody; Sebastian Zöllner; James G Wilson; L Adrienne Cupples; Cathy C Laurie; Cashell E Jaquish; Ryan D Hernandez; Timothy D O'Connor; Gonçalo R Abecasis Journal: Nature Date: 2021-02-10 Impact factor: 69.504
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