Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

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外文摘要：Recent advances in next-generation sequencing technology allow high-throughput RNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies.For model organisms with a reference genome,the first step in analysis of RNA-Seq data involves mapping of short-read sequences to the reference genome.Reference-guided transcriptome assembly is an optional step,which is recommended if the aim is to identify novel transcripts.Following read mapping,the primary interest of biologists in many RNA-Seq studies is the investigation of diferential expression between experimental groups.In this review,we discuss recent developments in RNA-Seq data analysis applied to model organisms,including methods and algorithms for direct mapping,reference-guided transcriptome assembly and differential expression analysis,and provide insights for the future direction of RNA-Seq.

外文关键词：

RNA-Seqmappingreference-guided transcriptome assemblydifferential expression analysis

作者：

Qiong-Yi Zhao、Jacob Gratten、Restuadi Restuadi、Xuan Li

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作者单位：

The University of Queensland, Queensland Brain Institute, St Lucia, QId 4072, Australia

Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences, Shanghai 200032, China

基金：

This work is supported by the National Health and Medical Research Council project grantsThis work is supported by the National Health and Medical Research Council project grantsNational Basic Research Program of ChinaNational Natural Science Foundation of China

项目编号：

APP1067795APP10878892012CB31650131571310

出版年：

2016

DOI：

10.1007/s40484-016-0060-7

定量生物学(英文版)

CSCD

ISSN：

年,卷(期)：2016.4(1)

参考文献量120