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首页> 外文期刊>Current Protocols in Bioinformatics >UNIT 11.15 Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing
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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.
机译：RNA测序（RNA-SEQ）是一种高通量技术，可为转录组提供独特的见解。它具有量化基因/同种型的各种应用以及检测非编码RNA，替代剪接和接头连接。理解整个转录组非常重要，以便彻底了解蜂窝系统。已经提出了几个RNA-SEQ分析管道迄今为止。但是，没有单一分析管道可以捕获整个转录组的动态。在这里，我们编译和呈现覆盖整个转录组分析的稳健和常用的分析管线，包括质量检查，读取的对准，差异基因/转录表达分析，发现隐秘拼接事件和可视化。突出显示并讨论了与每个步骤相关联的挑战，关键参数和可能的下游功能分析管道。本机提供了全面了解最先进的RNA-SEQ分析管道，并更加了解转录组。

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