biostudies-literatureVeerappa AMNIGMS NIH HHSNOSI supplement to the parent IDeA Networks of Biomedical Research Excellence (INBRE) Programbbae090https://www.ebi.ac.uk/biostudies/studies/S-EPMC11264300biostudies-literatureUnknown25(Supplement_1)Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) generates genome-wide chromatin accessibility profiles, providing valuable insights into epigenetic gene regulation at both pooled-cell and single-cell population levels. Comprehensive analysis of ATAC-seq data involves the use of various interdependent programs. Learning the correct sequence of steps needed to process the data can represent a major hurdle. Selecting appropriate parameters at each stage, including pre-analysis, core analysis, and advanced downstream analysis, is important to ensure accurate analysis and interpretation of ATAC-seq data. Additionally, obtaining and working within a limited computational environment presents a significant challenge to non-bioinformatic researchers. ThereforeBriefings in bioinformaticsCloudATAC: a cloud-based framework for ATAC-Seq data analysis.PMC11264300P20 GM103427NIH/NIGMS P20 GM103427Rowley MJKim ASethi SVeerappa AMBeaudry LGuda CMaggio AHawkins DSorgen PLfalseCloudATAC: a cloud-based framework for ATAC-Seq data analysis.Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) generates genome-wide chromatin accessibility profiles, providing valuable insights into epigenetic gene regulation at both pooled-cell and single-cell population levels. Comprehensive analysis of ATAC-seq data involves the use of various interdependent programs. Learning the correct sequence of steps needed to process the data can represent a major hurdle. Selecting appropriate parameters at each stage, including pre-analysis, core analysis, and advanced downstream analysis, is important to ensure accurate analysis and interpretation of ATAC-seq data. Additionally, obtaining and working within a limited computational environment presents a significant challenge to non-bioinformatic researchers. Therefore2024-01-01T00:00:00Z2024 Jul2025-06-01T01:15:29.654Z2025-06-01T01:15:29.654ZS-EPMC112643003904191010.1093/bib/bbae090