Plan or run ATAC-seq analysis to identify accessible DNA regions. Check sequencing quality, align reads, detect peaks, combine evidence across replicate samples, and prepare comparisons between conditions with quality summaries and visualization tracks.
Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.
Review the instructions the agent will receive before you install.
Use this skill for ATAC-seq accessibility analysis from FASTQ or BAM. If the assay is ChIP-seq, CUT&RUN, CUT&Tag, or antibody-targeted enrichment, use ngs-chip-cutrun-peaks-qc.
Confirm:
Prefer nf-core/atacseq for full reproducible processing. Use direct MACS2 only when BAMs are already aligned, duplicate/blacklist handling is known, and the user wants focused peak calling.
Preflight command:
python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline atacseq_peaks_qc --emit-install-plan
For compact read-level intake/QC, use the shared epigenomics execution package:
python plugins/ngs-analysis/scripts/run_fastq_assay_package.py \
--lane epigenomics_peaks \
--sample-sheet atac_samples.csv \
--execute
For local-light ATAC alignment, peaks, FRiP, TSS, bigWig tracks, and consensus peaks from FASTQ or prepared BAMs, use the dedicated ATAC runner:
python plugins/ngs-analysis/scripts/run_atacseq_peaks_qc.py \
--sample-sheet atac_samples.csv \
--bowtie2-index /refs/GRCh38/bowtie2/genome \
--genome-size hs \
--blacklist-bed /refs/GRCh38/blacklists/encode_blacklist.bed \
--tss-bed /refs/GRCh38/tss.bed \
--execute
This runner emits qc/atacseq_qc_summary.{tsv,json}, qc/atacseq_qc_dashboard.html, native SVG FRiP/peak and insert-size plots, browser-track handoff files under tracks/, and TSS profile/heatmap commands when --tss-bed is supplied. Add --run-motifs --motif-genome <genome> when HOMER motif enrichment should be part of the backend run.
It also emits resources/resource_plan.json, resource_manifest.tsv, resource_env.sh, and resource_readiness.md. The resource check is advisory by default for local-light runs; add --genome-build, --bundle-root <bundle>=<path>, and --require-resource-plan when missing registered reference bundles should block readiness.
For nf-core execution, use plugins/ngs-analysis/scripts/run_nfcore_pipeline.py --pipeline atacseq.
Review before biological interpretation:
Do not proceed to differential accessibility if replicate quality or metadata is insufficient.
Produce:
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