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).

In this tutorial we use an R / Bioconductor package ChIPseeker, to have a look at the ATAC / ChIP profiles, annotate peaks and visualise annotations. We will also perform functional annotation of peaks using clusterProfiler.

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) ... Open chromatin regions can be defined, for example, by standard peak calling of pseudo bulk ATAC-seq data. Further steps include data reduction with PCA and clustering of cells. [20] scATAC-seq matrices can be extremely large (hundreds of thousands of regions) ...

Jan 1, 2025 · In ATAC-seq data, we expect a multimodal distribution corresponding to categories such as NF fragments, mono-nucleosome fragments, tri-nucleosome fragments, and so on, with a main peak for NF fragments. Significant deviations from this pattern may indicate issues during library construction.

This includes four classes geared toward general ATAC-seq data processing: step-by-step analysis guides, raw sequence pipelines and workflows, quality control, and peak calling tools.

Sep 2, 2019 · In this training you have learned the general principles of ATAC-Seq data analysis. ATAC-Seq is a method to investigate the chromatin accessibility and the genome is treated with a transposase (enzyme) called Tn5. It marks open chromatin regions by cutting and inserting adapters for sequencing.

ATAC-Seq (Assay for Transposase-Accessible Chromatin with high-throughput Sequencing) is a method for determining chromatin accessibility across the genome. It utilizes a hyperactive Tn5 transposase to insert sequencing adapters into open chromatin regions (Fig. 1).

Conversely, in ATAC-seq, a shift is also required to align adjacent peaks into a single peak; this shift should be directed outward from the center of the peak. This adjustment accounts for the enrichment of reads at the flanking regions of the TF binding sites rather than at the central motif.

Dec 7, 2024 · ATAC-Seq is a powerful tool that combines the advantages of RNA-Seq and Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) to explore chromatin accessibility and the structure of regulatory...

Peaks are usually identified using either a reference bulk ATAC-seq data or by aggregating single-cell ATAC-seq data. To avoid missing information on rare cell types, peaks can also be called and merged from pseudo-bulk data, which aggregate cells from individual clusters.