ATAC-DEA: A Web-Based ATAC-Seq Data Differential Peak and Annotation Analysis Application

Abstract

Assay for transposase-accessible chromatin sequencing (ATAC-seq) has become one of the most widely used sequencing methods in studies of gene regulation, aiming to identify open chromatin sites and decipher how chromatin accessibility regulates gene expression. However, due to a lack of programming experience or minimal bioinformatics training, it is difficult for biologists to fully explore and interpret ATAC-seq results. Despite several available programs or websites that allow researchers to analyze and visualize ATAC-seq data, several limitations exist. ATAC-seq data differential expression analysis (ATAC-DEA), a web application that facilitates the exploration and visualization of differential peak analysis and annotation from ATAC-seq data, was developed (www.atac-dea.xyz:3838/ATAC-DEA). ATAC-DEA uses DiffBind and ChIPpeakAnno to process differential peak and annotation analysis results. ATAC-DEA has five features: (1) runs on a web server; (2) processes three files into one small file, which is used as the input for ATAC-DEA; (3) availability of various downloadable plots; (4) multifactor analysis and customized contrast model; and (5) annotates individual, overlapped, and differential peaks. It provides an easy-to-use user interface (UI) design for users to explore the data and modify the parameters interactively based on experimental purposes. ATAC-DEA allows biologists to generate user-friendly visual results from ATAC-seq downstream analysis.