ngs-atacseq-peaks-qc

# ATAC-seq Peaks QC 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`. ## Essential Inputs Confirm: - FASTQ/BAM inputs and paired-end status - organism, genome build, blacklist, and mitochondrial contig names - biological replicates, conditions, batches, and sample metadata - whether the target is QC only, peaks, consensus peaks, bigWigs, or differential accessibility - whether Tn5 shifting is handled by the chosen workflow - desired peak caller and downstream matrix generation ## Route 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: ```bash 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: ```bash 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: ```bash 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`. ## QC Gates Review before biological interpretation: - read depth, alignment rate, duplicate rate, and mitochondrial fraction - insert-size periodicity/nucleosome pattern - TSS enrichment and FRiP score when available - blacklist overlap and peak count per sample - replicate concordance and consensus peak support Do not proceed to differential accessibility if replicate quality or metadata is insufficient. ## Outputs Produce: - sample sheet and workflow command/profile - QC summary and failed-sample flags - narrowPeak/BED peak sets, consensus peaks, bigWigs, browser-track manifests, browser-track preview HTML, native QC dashboard/SVG plots, TSS plots, and peak-count matrix when requested - motif summary files when a motif backend is requested - differential-accessibility design and contrasts if applicable - caveats for low TSS enrichment, high mitochondrial reads, weak replicate concordance, or poor FRiP