Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add zongtingwei/Bioclaw_Skills_Hub --skill atac-seqgit clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_HubWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/atac-seq)<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/atac-seq"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/atac-seq/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/atac-seq"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/atac-seq.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00034 | $0.01058 |
| Opus 5 | $0.00017 | $0.00529 |
| Sonnet 5 | $0.00007 | $0.00212 |
| Haiku 4.5 | $0.00003 | $0.00106 |
Grade A, and why
atac-seq scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 165 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ATAC Seq
Version Compatibility
Reference examples assume:
macs33.0+samtools1.18+deepTools3.5+
Verify the runtime first:
- CLI:
macs3 --version,samtools --version,bamCoverage --version
Overview
Use this skill when the user needs:
- bulk ATAC-seq QC
- peak calling
- accessibility counting
- differential accessibility
- motif deviation or footprint follow-up
When To Use This Skill
- the task is bulk ATAC-seq rather than ChIP-seq
- TSS enrichment, fragment periodicity, or FRiP need review
- the output should include peaks, counts, and downstream accessibility summaries
Quick Route
- paired-end bulk ATAC: use
BAMPE - call peaks without control using ATAC-specific settings
- if TSS enrichment is poor, stop and flag data quality before interpretation
Progressive Disclosure
- Read technical_reference.md for QC gates and assay-specific caveats.
- Read commands_and_thresholds.md for peak-calling commands, thresholds, and output conventions.
Prerequisites
| Check | Guidance |
|---|---|
| uniquely mapped reads | >= 20M preferred for strong bulk ATAC |
| TSS enrichment | > 7 acceptable, > 10 strong |
| FRiP | > 0.2 often strong for good bulk ATAC |
Expected Inputs
- paired-end ATAC BAM or FASTQ
- reference genome
- sample groups for comparisons
Expected Outputs
results/peaks/sample_peaks.narrowPeakresults/matrix/consensus_peak_counts.tsvresults/diff_accessibility.tsvfigures/tss_enrichment.pdffigures/fragment_size_distribution.pdf
Starter Pattern
macs3 callpeak \
-t atac.bam \
-f BAMPE \
-g hs \
-n sample \
--nomodel \
--shift -100 \
--extsize 200 \
-q 0.01 \
--outdir results/peaks
Key Parameters
| Parameter | Typical value | Notes |
|---|---|---|
-f |
BAMPE |
paired-end ATAC should use fragment-aware mode |
--nomodel |
on | standard for ATAC |
--shift |
-100 |
common Tn5 offset convention |
--extsize |
200 |
common first-pass extension |
-q |
0.01 |
starting FDR threshold |
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 165 lines · 34 tokens per session scan A e0bf8b5ec840
atac-seq is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 34 tokens to every session and 1,058 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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