bio-atac-seq-atac-qc
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-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: bedtools 2.31+, deepTools 3.5+, numpy 1.26+, pandas 2.2+, picard 3.1+, pyBigWig 0.3+, pysam 0.22+, samtools 1.19+ 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 the example to match the actual API rather than retrying. # ATAC-seq Quality Control **"Check the quality of my ATAC-seq library"** → Evaluate fragment size distribution (nucleosome periodicity), TSS enrichment, FRiP, and library complexity to assess chromatin accessibility experiment quality. - CLI: `deeptools bamPEFragmentSize`, `picard CollectInsertSizeMetrics` - Python: `pysam` for custom fragment analysis ## Fragment Size Distribution **Goal:** Assess ATAC-seq library quality by visualizing the characteristic nucleosome periodicity in fragment sizes. **Approach:** Extract insert sizes from the BAM file using Picard o
- Version Compatibility
- Fragment Size Distribution
- TSS Enrichment Score
- Calculate TSS Enrichment Score
- FRiP (Fraction of Reads in Peaks)
- Mitochondrial Read Fraction
- Library Complexity (NRF, PBC1, PBC2)
- deepTools QC
- ATACseqQC (R)
- Comprehensive QC Report
- QC Thresholds
- Related Skills
Using Picard
java -jar picard.jar CollectInsertSizeMetrics \
Using samtools
samtools view -f 66 sample.bam | \
awk '{print sqrt($9^2)}' | \
sort | uniq -c | \
awk '{print $2"\t"$1}' > fragment_sizes.txt
Using deepTools
awk '$3=="transcript" {print $1"\t"$4-1"\t"$4"\t"$14"\t"0"\t"$7}' genes.gtf | \
tr -d '";' | sort -k1,1 -k2,2n > tss.bedWhat does the bio-atac-seq-atac-qc skill do?
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.