From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

By Feng Yan, David R. Powell, D. Curtis, N. Wong. Genome Biology, 2020

357 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e63babbf02db4f86375b52019345e6acb2f920e5

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Citations in the corpus

• Gene regulatory network inference in the era of single-cell multi-omics (2023, methodology): “In addition, single-cell data are by nature sparse and noisy, particularly for data obtained by scATAC-seq, and proper filters need to be used to ensure a minimum quality 148,149 .”