RNA-Seq: revelation of the messengers

被引：102

作者：

Van Verk, Marcel C. ^{[1
]}

Hickman, Richard ^{[1
]}

Pieterse, Corne M. J. ^{[1
,2
]}

Van Wees, Saskia C. M. ^{[1
]}

机构：

[1] Univ Utrecht, Dept Biol, NL-3584 CH Utrecht, Netherlands

[2] Ctr BioSyst Genom, NL-6700 AB Wageningen, Netherlands

来源：

TRENDS IN PLANT SCIENCE | 2013年 / 18卷 / 04期

基金：

欧洲研究理事会;

关键词：

DIFFERENTIAL EXPRESSION; ALIGNMENT;

D O I：

10.1016/j.tplants.2013.02.001

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significant hurdle for many biologists. Here, we put forward the concepts and considerations that are critical for RNA-Seq data analysis and provide a generic tutorial with example data that outlines the whole pipeline from next-generation sequencing output to quantification of differential gene expression.

引用

页码：175 / 179

页数：5

共 18 条

[1] Differential expression analysis for sequence count data [J].

Anders, Simon ;

Huber, Wolfgang .

GENOME BIOLOGY, 2010, 11 (10)

[2] Detecting differential usage of exons from RNA-seq data [J].

Anders, Simon ;

Reyes, Alejandro ;

Huber, Wolfgang .

GENOME RESEARCH, 2012, 22 (10) :2008-2017

[3]

Dillies M., 2012, BRIEF BIOINF

[4] Tools for mapping high-throughput sequencing data [J].

Fonseca, Nuno A. ;

Rung, Johan ;

Brazma, Alvis ;

Marioni, John C. .

BIOINFORMATICS, 2012, 28 (24) :3169-3177

[5] baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data [J].

Hardcastle, Thomas J. ;

Kelly, Krystyna A. .

BMC BIOINFORMATICS, 2010, 11

[6]

Katz Y, 2010, NAT METHODS, V7, P1009, DOI [10.1038/nmeth.1528, 10.1038/NMETH.1528]

[7] A COMPARISON OF STATISTICAL METHODS FOR DETECTING DIFFERENTIALLY EXPRESSED GENES FROM RNA-SEQ DATA [J].

Kvam, Vanessa M. ;

Lu, Peng ;

Si, Yaqing .

AMERICAN JOURNAL OF BOTANY, 2012, 99 (02) :248-256

[8] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [J].

Langmead, Ben ;

Trapnell, Cole ;

Pop, Mihai ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2009, 10 (03)

[9] RNA-Seq gene expression estimation with read mapping uncertainty [J].

Li, Bo ;

Ruotti, Victor ;

Stewart, Ron M. ;

Thomson, James A. ;

Dewey, Colin N. .

BIOINFORMATICS, 2010, 26 (04) :493-500

[10]

Li H, 2009, BIOINFORMATICS, V25, P1094, DOI [10.1093/bioinformatics/btp324, 10.1093/bioinformatics/btp100]

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