atac-seq

ATAC-seq analysis processes raw chromatin accessibility data into QC metrics, peak calls, and accessible region summaries. The workflow evaluates library quality, calls peaks using macs3 with ATAC-specific settings, and constructs consensus peak matrices across multiple samples.

Bulk ATAC-seq QC assessment requires reads depth, TSS enrichment, duplication rates, and FRiP scores. These metrics evaluate library complexity and signal quality, with results organized under the qc/ directory for straightforward quality evaluation.

Differential accessibility analysis builds a consensus peak matrix across samples to identify changes in chromatin accessibility. This workflow constructs matrices from called peaks and compares accessibility profiles to pinpoint significant differences.

Yes, macs3 is required for ATAC-specific peak calling to ensure robust peak identification. Downstream motif or footprint analysis follows peak detection to provide regulatory insight into accessible chromatin regions.

Yes, the ATAC-seq workflow requires samtools and deepTools alongside macs3. These dependencies support data processing, QC evaluation, and peak calling to generate organized outputs under results/ and qc/ directories.

ATAC-seq analysis is ideal for regulatory motif and footprint follow-up, converting raw signals into accessible region summaries. It processes bulk ATAC-seq data through QC, peak calling, and differential accessibility to enable downstream regulatory analysis.