RNA-seq reads 的差异表达分析：概述、分类和工具。

Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools.

出版信息

IEEE/ACM Trans Comput Biol Bioinform. 2020 Mar-Apr;17(2):566-586. doi: 10.1109/TCBB.2018.2873010. Epub 2018 Oct 1.

DOI:10.1109/TCBB.2018.2873010

Abstract

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 a descriptive comparison of tools used in each step of RNA-seq data analysis along with a discussion of important characteristics of 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.

摘要

RNA-seq 数据分析在转录组学研究中得到了广泛的应用，具有许多应用。我们从 RNA-seq 读取到差异表达分析的结果，综述了 RNA-seq 数据分析。此外，我们还对 RNA-seq 数据分析各个步骤中使用的工具进行了描述性比较，并讨论了这些工具的重要特征。还提供了工具的分类法。还讨论了 RNA-seq 数据的质量控制和可视化问题，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导，以及应该解决的研究问题和挑战。