Best Practices for Pre-Processing Large-Scale ATAC-Seq Data: Why Epidemiological Studies Demand Greater Stringency

Assay for transposase accessible chromatin using sequencing (ATAC-seq) and related techniques provide critical insight into the epigenetic mechanisms that regulate gene expression in health and disease. Accurate identification of biologically meaningful chromatin accessibility signals remains an underexplored analytical challenge. Advances in sequencing technologies have increased both the magnitude and complexity of ATAC-seq datasets, leading to demand for scalable, reproducible and robust computational analysis frameworks. Peak calling, which identifies regions of chromatin accessibility, is a critical step that underpins all downstream quantitative analyses. However, there is a lack of consensus regarding the optimal peak calling strategy. Here, we present a novel bioinformatics pipeline PIPPA (Pipeline for Integrative Peak calling in Population-scale ATAC-seq), for quality control and peak set curation of large-scale ATAC-seq datasets. Using two independent cell-type sorted ATAC-seq datasets, we show that peak calling performance is dataset-dependent and that no single significance threshold performs optimally across all scenarios. We provide practical recommendations for parameters to generate high-confidence chromatin accessibility profiles. Our peak calling approach is applicable for other genome wide epigenomic assays such as ChIP-seq and CUT&Tag. By standardising this process, the PIPPA pipeline enhances epidemiological studies focused in identifying epigenetic dysregulation associated with development and disease.