Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.

中文翻译：

---

DNase-seq数据分析的实用指南：从数据管理到常见应用程序。

脱氧核糖核酸酶I（DNase I）的超敏性位点测序（DNase-seq）已被广泛用于确定染色质的可及性及其潜在的调控词典。但是，探索DNase-seq数据需要复杂的下游生物信息学分析。在这项研究中，我们首先回顾了DNase-seq数据分析中所有主要步骤的计算方法，包括实验设计，质量控制，读取比对，峰调用，顺式调控元件注释，基因组足迹和可视化。突出显示了与每个步骤相关的挑战。接下来，我们通过集成其中的一些工具，为DNase-seq数据分析提供了实用指南和计算管道。我们还讨论了竞争技术以及该管道在类似实验数据分析中的潜在应用。