Ather Syed Hussain, Awe Olaitan Igbagbo, Butler Thomas J, Denka Tamiru, Semick Stephen Andrew, Tang Wanhu, Busby Ben
National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
F1000Res. 2018 May 22;7. doi: 10.12688/f1000research.14880.4. eCollection 2018.
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( https://github.com/NCBI-Hackathons/seqacademy, http://www.seqacademy.org/). This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
基因表达定量和基因转录本结构表征是分子生物学的核心问题。RNA测序（RNA-Seq）和染色质免疫沉淀测序（ChIP-Seq）是重要的方法，但对于初学者来说可能繁琐且难学。为了向感兴趣的学生和科学家传授如何分析RNA-Seq和ChIP-Seq数据，我们提供了一个从头到尾分析RNA-Seq和ChIP-Seq数据的教程：SeqAcademy（https://github.com/NCBI-Hackathons/seqacademy，http://www.seqacademy.org/）。这个用户友好的流程完全用Markdown语言编写，强调使用公开可用的RNA-Seq和ChIP-Seq数据，并将流行工具串联起来，弥合原始测序读数与生物学见解之间的差距。我们通过一个生物学实例——一个先前发表的酵母实验，展示了各种RNA-Seq和ChIP-Seq分析步骤的实际和概念性考量。这项工作通过向新手生物信息学家温和介绍RNA-Seq和ChIP-Seq分析的关键组成部分，对为高级用户设计的现有复杂RNA-Seq和ChIP-Seq流程起到补充作用。总之，这个文档完善的流程将向初学生物信息学家介绍最先进的RNA-Seq和ChIP-Seq分析工具，并有助于促进对数量不断增长的公共RNA-Seq和ChIP-Seq数据的分析。
