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).

This end-to-end tutorial will guide you through every step of ATAC-seq data analysis. We’ll show you how to set up your computing environment, fetch the raw sequencing data, perform read mapping, peak calling, and differential accessibility analysis, and …

Feb 12, 2025 · The process of single cell ATAC-seq involves several critical steps that ensure accurate mapping of chromatin accessibility. These steps isolate individual cells, tag accessible chromatin regions, and prepare samples for sequencing, allowing researchers to gain insights into the epigenetic landscape of each cell.

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. [1] In 2013, the technique was first described as an alternative advanced method …

Roadmap of a typical ATAC-seq analysis. Four major steps are listed, including pre-analysis, core analysis, advanced analysis, and integration with multiomics data. Pre-analyses include pre-alignment QC, alignment and post-alignment processing, and …

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 (Figure 1).

Feb 6, 2025 · The initial step in the ATAC-seq protocol involves meticulous sample collection and cell preparation, which lays the groundwork for accurate chromatin accessibility analysis. The choice of sample type—whether tissue, cultured cells, or …

Analyzing ATAC-seq data involves several important steps: Quality Control and Preprocessing: The initial step in bioinformatics analysis is to assess the quality of the sequencing reads. Tools like FastQC help identify issues such as low-quality bases or adapter contamination.

FastQC reports can be generated for all samples to assess sequence quality, GC content, duplication rates, length distribution, K-mer content and adapter contamination. In ATAC-seq data, it is likely that Nextera sequencing adapters will be over-represented.

Feb 9, 2021 · Below, we give a short overview of the ATAC-Seq protocol, which can be divided up into two main parts: cell preparation and transposition. As a first step, the cells need to be harvested.