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.
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Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.
安装前可以查看交给 AI 代理的指令内容。
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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Review charts, diagrams, and dashboards for accessibility, including color contrast, keyboard access, and text alternatives. Get specific guidance for preserving key findings in screen readers, static exports, and reduced-motion views.
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Give a photo collection a consistent look using Adobe tools to adjust color, tone, presets, and optional crops. Review a before-and-after sample before processing the full set, then receive links to the edited images.
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Visualize a logo, sketch, or design on products such as mugs, shirts, and business cards. Review a pilot image, generate a visually consistent set, and collect the results on a shareable Firefly Board.
中文简介正在准备中。当前显示英语简介。
Prepare images and videos for social platforms using Adobe tools. Create image crops that keep the subject in view, expand backgrounds when available, preview a full-set sample, and resize videos while preserving their aspect ratio.
中文简介正在准备中。当前显示英语简介。
Create flyers, social posts, business cards, and other visuals from Adobe Express templates. Choose a template, customize its text and background color, and receive a design link, with additional editing and export options depending on the available tools.
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Turn an uploaded video into three highlight edits with Adobe Quick Cut. Choose a target length and style, then compare versions that feature different moments and download the ones you prefer.
中文简介正在准备中。当前显示英语简介。