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


Type

Article

Change log

Authors

Conesa, Ana 
Tarazona, Sonia 
Gomez-Cabrero, David 
Cervera, Alejandra 

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.

Description

Keywords

Alternative Splicing, Base Sequence, Gene Expression Profiling, Gene Fusion, Genomics, High-Throughput Nucleotide Sequencing, RNA, Sequence Analysis, RNA, Software

Journal Title

Genome Biol

Conference Name

Journal ISSN

1474-7596
1474-760X

Volume Title

17

Publisher

Springer Science and Business Media LLC
Sponsorship
Medical Research Council (MC_PC_12009)