Computational Analyses and Challenges of Single-cell ATAC-seq.

ABSTRACT: Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful technique to study cell-specific epigenetic landscapes and to provide a multidimensional portrait of gene regulation. However, low genomic coverage per cell results in intrinsic data sparsity and missing-data issues, presenting unique methodological challenges. Consequently, numerous computational methods and techniques have been developed to address these challenges. This review provides a concise overview of published workflows for scATAC-seq analysis, covering preprocessing through downstream analysis including quality control, alignment, peak calling, dimensionality reduction, clustering, gene regulation score calculation, cell type annotation, and multiomics integration. Addi

SUBMITTER: Wang C 

PROVIDER: S-EPMC12753137 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature