转录组
RNA序列
RNA剪接
计算生物学
管道(软件)
生物
选择性拼接
核糖核酸
基因
计算机科学
遗传学
基因表达
基因亚型
程序设计语言
作者
Hari Krishna Yalamanchili,Ying‐Wooi Wan,Zhandong Liu
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. © 2017 by John Wiley & Sons, Inc.
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