UNIT 11.15 Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing

Hari Krishna Yalamanchili; Ying-Wooi Wan; Zhandong Liu

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UNIT 11.15 Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing

机译：单元11.15 RNA-SEQ实验数据分析管道：从差异表达到密码拼接

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摘要

RNA sequencing (RNA-seq) is a high-throughput technology that provides unique insights into the transcriptome. It has a wide variety of applications in quantifying genes/isoforms and in detecting non-coding RNA, alternative splicing, and splice junctions. It is extremely important to comprehend the entire transcriptome for a thorough understanding of the cellular system. Several RNA-seq analysis pipelines have been proposed to date. However, no single analysis pipeline can capture dynamics of the entire transcriptome. Here, we compile and present a robust and commonly used analytical pipeline covering the entire spectrum of transcriptome analysis, including quality checks, alignment of reads, differential gene/transcript expression analysis, discovery of cryptic splicing events, and visualization. Challenges, critical parameters, and possible downstream functional analysis pipelines associated with each step are highlighted and discussed. This unit provides a comprehensive understanding of state-of-the-art RNA-seq analysis pipeline and a greater understanding of the transcriptome.

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来源
《Current Protocols in Bioinformatics》 |2017年第59期|共22页
作者
Hari Krishna Yalamanchili; Ying-Wooi Wan; Zhandong Liu;
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作者单位

Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas;

Bioinformatics Core Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital Houston Texas;

Computational and Integrative Biomedical Research Center Baylor College of Medicine Houston Texas;

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原文格式 PDF
正文语种 eng
中图分类遗传学;
关键词
RNA-seq; differential gene expression; differential isoform usage; alternative splicing; cryptic splicing;

机译：RNA-SEQ;差异基因表达;差分同种型使用;替代剪接;隐秘拼接;

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1. Mapping and differential expression analysis from short-read RNA-Seq data in model organisms [J] . Qiong-Yi Zhao, Jacob Gratten, Restuadi Restuadi, 定量生物学（英文版） . 2016,第001期
2. Mapping and differential expression analysis from short-read RNA-Seq data in model organisms [J] . Qiong-Yi, Zhao1, Jacob, 中国电气与电子工程前沿：英文版 . 2016,第001期
3. Differential expression analyses for single-ce RNA-Seq： old questions on new data [J] . Zhun Miao1, Xuegong Zhang12 中国电气与电子工程前沿：英文版 . 2016,第004期
4. UNIT 11.15 Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing [J] . Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu Current Protocols in Bioinformatics . 2017,第Suppla59期

机译：单元11.15 RNA-SEQ实验数据分析管道：从差异表达到密码拼接
5. Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing [J] . Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu Current Protocols in Bioinformatics . 2017,第Suppla59期

机译：用于RNA-SEQ实验的数据分析管道：从差异表达到密码拼接
6. SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing [J] . Wang Xi, Cairns Murray J. Bioinformatics . 2014,第12期

机译：SeqGSEA：用于整合差异表达和剪接的RNA-Seq数据的基因集富集分析的生物导体包装
7. A Unified Model for Robust Differential Expression Analysis of RNA-Seq Data [C] . Kefei Liu, Li Shen, Hui Jiang IEEE International Conference on Bioinformatics and Biomedicine . 2018

机译：RNA-Seq数据鲁棒差异表达分析的统一模型
8. An Isoform-free Model for Differential Expression Analysis in RNA-seq Data. [D] . Liu, Yang. 2016

机译：RNA序列数据中差异表达分析的无异构形式模型。
9. Data analysis pipeline for RNA-seq experiments: From differential expression to cryptic splicing [O] . Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu -1

机译：RNA-seq实验的数据分析管道：从差异表达到隐秘剪接
10. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [O] . Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth 2016

机译：从读到基因到途径：使用rsubread和edger准可能性管道的RNA-SEQ实验的差异表达分析
11. Messenger RNA Isolation From PAXgene Blood RNA Tubes for RNA-seq Differential Analysis After Traumatic Brain Injury. [R] . Neill, M. J. 2018

机译：来自paXgene血液RNa管的信使RNa分离用于创伤性脑损伤后的RNa-seq差异分析。

UNIT 11.15 Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing

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