Feb 3, 2020 · 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, …

A step-by-step pipeline for the analysis of ATAC-seq data (the a ssay for t ransposase- a ccessible c hromatin with seq uencing), written by the Cebola Lab. The resources used to …

Here, we explain the fundamentals of ATAC-seq data processing, summarize common analysis approaches, and review computational tools to provide recommendations for different research questions.

Oct 26, 2020 · Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main...

Jan 1, 2025 · ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a method to study genome accessibility. It enables researchers to identify regions of the genome accessible to transcription machinery—indicating potential transcriptional activity—and regions that are condensed and transcriptionally inactive.

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).

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 …

Sep 2, 2019 · 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.

This review provides a brief overview of the general principle and production of single-cell ATAC-seq followed by an explanation of the data analysis process from the general workflow to downstream analysis for different applications.

ATAC-Seq analysis is used to investigate a number of chromatin-accessibility signatures. The most common use is nucleosome mapping experiments, [3] but it can be applied to mapping transcription factor binding sites, [13] adapted to map DNA methylation sites, [14] or combined with sequencing techniques.