bio-atac-seq-atac-peak-calling
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-atac-peak-calling --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: Bowtie2 2.5.3+, MACS3 3.0+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - 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 Peak Calling **"Call peaks from my ATAC-seq data"** → Identify open chromatin regions using ATAC-specific parameters (no input control, shifted Tn5 cut sites, paired-end mode). - CLI: `macs3 callpeak -t atac.bam -f BAMPE -g hs --nomodel --shift -75 --extsize 150` ## Basic MACS3 for ATAC-seq **Goal:** Identify open chromatin regions from ATAC-seq data using ATAC-specific peak calling parameters. **Approach:** Run MACS3 in paired-end mode with Tn5 shift correction, no model building, and duplicate retention since ATAC-seq generates natural duplicates at accessible sites. ```bash # Standard ATAC-seq peak calling macs3 callpeak \ -t sample.bam \ -f BAMPE \ -g hs \ -n sample \ --outdir peaks/ \ -q 0.05 \ --nomodel \ --shift -75 \ --extsize 150 \ --keep-dup all \ -B ``` ## Key ATA
- Version Compatibility
- Basic MACS3 for ATAC-seq
- Key ATAC-seq Parameters
- Why These Parameters?
- Paired-End vs Single-End
- Call Peaks on NFR Only
- Broad Peaks (Optional)
- Batch Processing
- Output Files
- narrowPeak Format
- Convert to BigWig
- Merge Replicates
- IDR for Replicate Consistency
- Related Skills
Standard ATAC-seq peak calling macs3 callpeak \ Explained parameters Paired-end (recommended for ATAC) macs3 callpeak -f BAMPE -t sample.bam ... Single-end (less common) macs3 callpeak -f BAM -t sample.bam \ samtools view -h sample.bam | \ awk 'substr($0,1,1)=="@" || ($9>0 && $9<100) || ($9<0 && $9>-100)' | \ samtools view -b > nfr.bam
What does the bio-atac-seq-atac-peak-calling skill do?
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-atac-peak-calling --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.