Analysis of RNA-sequence (RNA-seq) data is widely used in transcriptomic studies and it has many applications. We review RNA-seq data analysis from RNA-seq reads to the results of differential expression analysis. In addition, we perform descriptive comparison of tools used in each step of RNA-seq data analysis along with a discussion of important aspects for these tools. A taxonomy of tools is also provided. A discussion of issues in quality control and visualization of RNA-seq data is also included along with useful tools. Finally, we provide some guidelines for the RNA-seq data analyst, along with research issues and challenges which should be addressed.

中文翻译：

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RNA-seq读物的差异表达分析：概述，分类法和工具。

RNA序列（RNA-seq）数据分析广泛用于转录组学研究，并且有许多应用。我们回顾了从RNA序列读取到差异表达分析结果的RNA序列数据分析。此外，我们对在RNA-seq数据分析的每个步骤中使用的工具进行描述性比较，并讨论这些工具的重要方面。还提供了工具分类。还包括有关质量控制和RNA-seq数据可视化的问题的讨论以及有用的工具。最后，我们为RNA-seq数据分析人员提供了一些指南，以及应解决的研究问题和挑战。