esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Chromatin accessibility is crucial for understanding gene regulation.
• Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a key method for genome-wide accessibility studies.
• Systematic analysis of ATAC-seq data presents computational challenges.

Purpose of the Study:

• To introduce esATAC, an integrated R/Bioconductor package for streamlined ATAC-seq data analysis.
• To provide a user-friendly tool for comprehensive analysis, from raw data processing to downstream interpretation.
• To facilitate both preset and customized ATAC-seq analysis pipelines.

Main Methods:

• Development of an R/Bioconductor package named esATAC.
• Implementation in R and C++ for efficiency.
• Inclusion of modules for raw data processing, quality control, peak calling, enrichment analysis, and transcription factor footprinting.

Main Results:

• esATAC offers a systematic and integrated approach to ATAC-seq data analysis.
• The package supports automated pipelines via a single command line.
• Flexible interfaces allow for the construction of customized analysis workflows.

Conclusions:

• esATAC simplifies and enhances the systematic analysis of ATAC-seq data.
• The package provides a robust platform for researchers studying genome-wide chromatin accessibility.
• esATAC is open-source and available for Linux, macOS, and Windows.