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PMID: 26813401 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Review

A survey of best practices for RNA-seq data analysis.

Genome biology ·Vol. 17 ·2016-01-26 ·Pages 13

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A

Abstract

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.

MeSH Terms
Alternative Splicing/genetics Base Sequence Gene Expression Profiling Gene Fusion/genetics Genomics High-Throughput Nucleotide Sequencing/methods RNA/genetics Sequence Analysis, RNA/methods Software
Chemicals
RNA
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Conesa Ana
Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA. [email protected]. | Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain. [email protected].
Madrigal Pedro
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. [email protected]. | Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, CB2 0SZ, UK. [email protected].
Tarazona Sonia
Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain. | Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, 46020, Valencia, Spain.
Gomez-Cabrero David
Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 77, Stockholm, Sweden. | Center for Molecular Medicine, Karolinska Institutet, 17177, Stockholm, Sweden. | Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176, Stockholm, Sweden. | Science for Life Laboratory, 17121, Solna, Sweden.
Cervera Alejandra
Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, 00014, Helsinki, Finland.
McPherson Andrew
School of Computing Science, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada.
Szcześniak Michał Wojciech
Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland.
Gaffney Daniel J
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Elo Laura L
Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.
Zhang Xuegong
Key Lab of Bioinformatics/Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, 100084, China. | School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Mortazavi Ali
Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA. [email protected]. | Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA. [email protected].
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/s13059-016-0881-8
Email
[email protected]
[email protected]
[email protected]
Published
2016-01-26
Epub
2016-00-26
Pages
13
Language
English
Region
England
NLM ID
100960660
PMCID
PMC4728800
Subset
IM
Grants
Wellcome Trust · United Kingdom
NIGMS NIH HHS · DP2 GM111100 · United States
Medical Research Council · MC_PC_12009 · United Kingdom
Corrections
ErratumIn
PMID: 27565134
External Links
PubMed source DOI: 10.1186/s13059-016-0881-8 PMC Full Text View journal details
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