From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
Feng Yan, David R Powell, David J Curtis, Nicholas C Wong
Genome Biology | BMC | Published : 2020
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 d..View full abstract
FY acknowledges funding support from Monash University (Monash Graduate Scholarship and Monash International Postgraduate Research Scholarship).