A Review on The Processing and Analysis of Next-generation RNA-seq Data

被引：14

作者：

Wang Xi ^{[1
,2
]}

Wang Xiao-Wo ^{[1
,2
]}

Wang Li-Kun ^{[1
,2
,3
]}

Feng Zhi-Xing ^{[1
,2
]}

Zhang Xue-Gong ^{[1
,2
]}

机构：

[1] Tsinghua Univ, Minist Educ, Key Lab Bioinformat, Beijing 100084, Peoples R China

[2] Tsinghua Univ, Bioinformat Div, TNLIST Dept Automat, Beijing 100084, Peoples R China

[3] Jilin Univ, Coll Comp Sci & Technol, Changchun 130012, Peoples R China

来源：

PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS | 2010年 / 37卷 / 08期

基金：

中国国家自然科学基金;

关键词：

high-throughput RNA sequencing; transcriptome; gene expression; data processing and analysis; bioinformatics; GENE-EXPRESSION; CHIP-SEQ; FLUORESCENT NUCLEOTIDE; SEQUENCE; TRANSCRIPTOME; ALIGNMENT; TOOL; IDENTIFICATION; VISUALIZATION; CHALLENGES;

D O I：

10.3724/SP.J.1206.2009.00151

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

With the rapid development of the next-generation sequencing (NGS) technology, high-throughput RNA sequencing or RNA-seq is becoming a key experimental approach in the study of gene expression and transcriptome. The overwhelming amount of RNA-seq data brings new opportunities and challenges for bioinformatics. The efficient and effective processing and analysis of RNA-seq data is becoming the bottleneck for turning the possibilities provided by the new technology into real scientific discovery. A general description of the typical RNA-seq protocol was given. A complete review of major methods and available software in the processing and analysis of RNA-seq data were presented, using the Illumina/Solexa platform as an example. Questions that are still open and awaiting further research are also discussed.

引用

页码：834 / 846

页数：13

共 87 条

[1]

[Anonymous], 1994, 124 DIG SYST RES CTR

[2] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[3] De novo transcriptome assembly with ABySS [J].

Birol, Inanc ;

Jackman, Shaun D. ;

Nielsen, Cydney B. ;

Qian, Jenny Q. ;

Varhol, Richard ;

Stazyk, Greg ;

Morin, Ryan D. ;

Zhao, Yongjun ;

Hirst, Martin ;

Schein, Jacqueline E. ;

Horsman, Doug E. ;

Connors, Joseph M. ;

Gascoyne, Randy D. ;

Marra, Marco A. ;

Jones, Steven J. M. .

BIOINFORMATICS, 2009, 25 (21) :2872-2877

[4] Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing [J].

Birzele, Fabian ;

Schaub, Jochen ;

Rust, Werner ;

Clemens, Christoph ;

Baum, Patrick ;

Kaufmann, Hitto ;

Weith, Andreas ;

Schulz, Torsten W. ;

Hildebrandt, Tobias .

NUCLEIC ACIDS RESEARCH, 2010, 38 (12) :3999-4010

[5] A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly [J].

Blankenberg, Daniel ;

Taylor, James ;

Schenck, Ian ;

He, Jianbin ;

Zhang, Yi ;

Ghent, Matthew ;

Veeraraghavan, Narayanan ;

Albert, Istvan ;

Miller, Webb ;

Makova, Kateryna D. ;

Hardison, Ross C. ;

Nekrutenko, Anton .

GENOME RESEARCH, 2007, 17 (06) :960-964

[6] Sex-specific and lineage-specific alternative splicing in primates [J].

Blekhman, Ran ;

Marioni, John C. ;

Zumbo, Paul ;

Stephens, Matthew ;

Gilad, Yoav .

GENOME RESEARCH, 2010, 20 (02) :180-189

[7] Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays [J].

Bloom, Joshua S. ;

Khan, Zia ;

Kruglyak, Leonid ;

Singh, Mona ;

Caudy, Amy A. .

BMC GENOMICS, 2009, 10

[8] Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver [J].

Brunner, Alayne L. ;

Johnson, David S. ;

Kim, Si Wan ;

Valouev, Anton ;

Reddy, Timothy E. ;

Neff, Norma F. ;

Anton, Elizabeth ;

Medina, Catherine ;

Nguyen, Loan ;

Chiao, Eric ;

Oyolu, Chuba B. ;

Schroth, Gary P. ;

Absher, Devin M. ;

Baker, Julie C. ;

Myers, Richard M. .

GENOME RESEARCH, 2009, 19 (06) :1044-1056

[9] RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data [J].

Cloonan, Nicole ;

Xu, Qinying ;

Faulkner, Geoffrey J. ;

Taylor, Darrin F. ;

Tang, Dave T. P. ;

Kolle, Gabriel ;

Grimmond, Sean M. .

BIOINFORMATICS, 2009, 25 (19) :2615-2616

[10] The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants [J].

Cock, Peter J. A. ;

Fields, Christopher J. ;

Goto, Naohisa ;

Heuer, Michael L. ;

Rice, Peter M. .

NUCLEIC ACIDS RESEARCH, 2010, 38 (06) :1767-1771

← 1 2 3 4 5 6 7 8 9 →