ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Assays for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a key technique for genome-wide chromatin accessibility analysis.
• While ATAC-seq offers advantages like speed and low cell input, robust quality assurance is crucial for experimental success.
• Existing tools lack comprehensive functionalities for preprocessing and quality assessment of aligned ATAC-seq data.

Purpose of the Study:

• To develop a Bioconductor package, ATACseqQC, for streamlined preprocessing and quality assessment of ATAC-seq data.
• To provide researchers with easily generated diagnostic plots for evaluating ATAC-seq data quality.
• To offer guidelines for ideal ATAC-seq data characteristics.

Main Methods:

• Development of the ATACseqQC Bioconductor package.
• Implementation of functions for preprocessing aligned ATAC-seq data.
• Demonstration of package utilities using 25 public ATAC-seq datasets.

Main Results:

• The ATACseqQC package provides essential functions for ATAC-seq data preprocessing.
• It generates diagnostic plots to facilitate rapid quality assessment.
• The package was validated using multiple public datasets, demonstrating its utility.

Conclusions:

• ATACseqQC successfully preprocesses and assesses ATAC-seq datasets.
• The diagnostic plots aid in evaluating experimental quality and selecting high-quality public data.
• The software is freely available, supporting reliable ATAC-seq research.