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

Zhao, Qiong-Yi, Gratten, Jacob, Restaudi, Restuadi and Li, Xuan (2016) Mapping and differential expression analysis from short-read RNA-Seq data in model organisms. Quantitative Biology, 4 1: 22-35. doi:10.1007/s40484-016-0060-7

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Author Zhao, Qiong-Yi
Gratten, Jacob
Restaudi, Restuadi
Li, Xuan
Title Mapping and differential expression analysis from short-read RNA-Seq data in model organisms
Journal name Quantitative Biology   Check publisher's open access policy
ISSN 2095-4689
2095-4697
Publication date 2016-03-01
Year available 2016
Sub-type Article (original research)
DOI 10.1007/s40484-016-0060-7
Open Access Status Not yet assessed
Volume 4
Issue 1
Start page 22
End page 35
Total pages 14
Place of publication Heidelberg, Germany
Publisher Springer
Language eng
Abstract 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 differential 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.
Keyword RNA-Seq
Mapping
Reference-guided transcriptome assembly
Differential expression analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Brain Institute Publications
 
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Created: Fri, 19 Aug 2016, 01:39:19 EST by Susan Day on behalf of Queensland Brain Institute