Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia.
Genome Biol. 2020 Feb 3;21(1):22. doi: 10.1186/s13059-020-1929-3.
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis). We also review the reconstruction of transcriptional regulatory networks with multiomics data and highlight the current challenges of each step. Finally, we describe the potential of single-cell ATAC-seq and highlight the necessity of developing ATAC-seq specific analysis tools to obtain biologically meaningful insights.
转座酶可及染色质测序（ATAC-seq）分析广泛用于研究染色质生物学，但目前尚未完成对分析工具的全面综述。在这里，我们讨论了 ATAC-seq 数据分析的主要步骤，包括预处理（质量检查和比对）、核心分析（峰调用）和高级分析（峰差异分析和注释、基序富集、足迹分析和核小体位置分析）。我们还回顾了利用多组学数据重建转录调控网络，并强调了每个步骤的当前挑战。最后，我们描述了单细胞 ATAC-seq 的潜力，并强调了开发特定于 ATAC-seq 的分析工具以获得有生物学意义的见解的必要性。
