Department of Genetics, Stanford University, Stanford, CA, USA.
Methods Mol Biol. 2021;2243:183-226. doi: 10.1007/978-1-0716-1103-6_10.
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Thanks to its great utility, it is now being applied to map active chromatin in the context of a very wide diversity of biological systems and questions. In the course of these studies, considerable experience working with ATAC-seq data has accumulated and a standard set of computational tasks that need to be carried for most ATAC-seq analyses has emerged. Here, we review and provide examples of common such analytical procedures (including data processing, quality control, peak calling, identifying differentially accessible open chromatin regions, and variable transcription factor (TF) motif accessibility) and discuss recommended optimal practices.
ATAC-seq 分析已成为研究真核生物中可及染色质区域和追踪顺式调控元件 (cREs) 活性的最有用、最通用和适应性最强的方法。由于其巨大的实用性，现在正被应用于在非常广泛的生物系统和问题的背景下绘制活性染色质图谱。在这些研究过程中，积累了大量的 ATAC-seq 数据处理经验，并且出现了一套用于大多数 ATAC-seq 分析的标准计算任务。在这里，我们回顾并提供了常见分析程序的示例（包括数据处理、质量控制、峰调用、识别差异可及的开放染色质区域以及可变转录因子 (TF) 基序可及性），并讨论了推荐的最佳实践。
