Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance-Reference-Cited by-同舟云学术

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Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance

Published:2018-11-14 Issue:1 Volume:19 Page:
ISSN:1471-2105
Container-title:BMC Bioinformatics
language:en
Short-container-title:BMC Bioinformatics

Author:

Baccarella Alyssa,Williams Claire R.,Parrish Jay Z.,Kim Charles C.^ORCID

Funder

University of California, San Francisco, Center for AIDS Research

National Institute of Allergy and Infectious Diseases

National Eye Institute

National Institute of Diabetes and Digestive and Kidney Diseases

National Institute of Neurological Disorders and Stroke

University of Washington

National Science Foundation

ACCMA

Schoeneman Scholarship

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology

Link

http://link.springer.com/content/pdf/10.1186/s12859-018-2445-2.pdf

Reference46 articles.

1. Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol. BioMed Central. 2010;11:220.

2. Fonseca NA, Marioni J, Brazma A, Salzberg S, Zaleski C. RNA-Seq Gene Profiling - A Systematic Empirical Comparison. Provart NJ, editor. PLoS One. Public Libr Sci; 2014;9:e107026.

3. Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, et al. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res Oxford University Press. 2012;40:10084–97.

4. Seyednasrollah F, Laiho A, Elo LL. Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform. 2015;16:59–70.

5. Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, et al. A benchmark for RNA-seq quantification pipelines. Genome Biol. BioMed Central. 2016;17:74.

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