bio-atac-seq-atac-qc
ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
npx skills add BioTender-max/awesome-bio-agent-skills --skill atac-qc --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: deepTools 3.5+, Picard 3.1+, samtools 1.19+, bedtools 2.31+, ATACseqQC 1.26+, pysam 0.22+, pyBigWig 0.3+, numpy 1.26+, pandas 2.2+, MultiQC 1.21+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt. # ATAC-seq Quality Control **"Does my ATAC library pass ENCODE quality criteria?"** -> Compute the seven canonical metrics (depth, alignment rate, mitochondrial fraction, library complexity, fragment-size periodicity, TSS enrichment, FRiP) and compare against ENCODE 4 thresholds, then diagnose failures. - CLI: `picard CollectInsertSizeMetrics`, `samtools flagstat`, `samtools idxstats` - CLI: `deeptools plotFingerprint`, `computeMatrix reference-point` + `plotProfile` - R: `ATACseqQC::TSSEscore`, `ATACseqQC::fragSizeDist`, `ATACseqQC::PTscore` - Python: custom NRF/PBC from coordinate hash;
- Version Compatibility
- ENCODE 4 ATAC-seq Acceptance Thresholds
- TSS Enrichment: ENCODE Method vs ATACseqQC Method
- Fragment-Size Periodicity Patterns
- Per-Metric Failure Modes
- Mitochondrial fraction > 50%
- NRF / PBC1 / PBC2 below threshold
- TSS enrichment < 5
- FRiP < 0.2
- Replicate correlation < 0.85
- Library Complexity (NRF, PBC1, PBC2)
- Cross-Replicate QC
- Library Complexity Extrapolation (preseq)
- Sex-Chromosome QC
Spearman correlation (more robust than Pearson for ATAC)
multiBamSummary bins -bs 10000 -p 8 \
plotCorrelation -in multi.npz \
Fingerprint (per-bin signal cumulative -- diagonal = no enrichment, sharp curve = good)
plotFingerprint -p 8 -b rep1.bam rep2.bam rep3.bam \
preseq c_curve -B sample.bam -o sample.ccurve.tsv -s 1e6
preseq lc_extrap -B sample.bam -o sample.lcextrap.tsv -e 200000000 -s 5000000
chrY read fraction
samtools idxstats sample.bam | awk '$1=="chrY"{print $3 / $2}' # reads per bp
XIST locus accessibility (chrX:73820651-73852723 in hg38)What does the bio-atac-seq-atac-qc skill do?
ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill atac-qc --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.