ATACseqQC

ATACseqQC performs quality control and preprocessing of Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) aligned datasets to assess and improve chromatin accessibility data quality for downstream analyses.

Key Features:

• Diagnostic Plots Generation: Generates diagnostic plots to evaluate ATAC-seq data quality and identify issues in aligned datasets.
• Preprocessing Functions: Provides preprocessing functions for aligned ATAC-seq datasets to prepare reads for peak calling analyses.
• Guidelines for Ideal Data Quality: Describes expected characteristics of diagnostic plots to assess dataset quality and to aid selection from public repositories such as the Gene Expression Omnibus (GEO).
• Comprehensive QC Workflow: Integrates wet lab quality-control metrics with in silico assessments for thorough evaluation of chromatin accessibility experiments.

Scientific Applications:

• Genome-wide chromatin accessibility analysis: Enables genome-wide analysis of chromatin accessibility by validating ATAC-seq dataset quality prior to downstream analyses.
• Data quality assurance to prevent misinterpretation: Detects low-quality datasets to reduce the risk of erroneous biological conclusions from ATAC-seq experiments.
• Applications with limited input material: Supports studies using small cell numbers or requiring rapid and sensitive chromatin accessibility assessments by verifying dataset integrity.

Methodology:

Combines diagnostic plotting with preprocessing of aligned ATAC-seq datasets and was demonstrated on 25 publicly available ATAC-seq datasets from four distinct studies.