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bio-chipseq-qc

Maintainer FreedomIntelligence · Last updated April 1, 2026

ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.

OpenClawNanoClawAnalysisReproductionbio-chipseq-qc🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinchip

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-qc

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • CLI: deeptools plotFingerprint, phantompeakqualtools run_spp.R.
  • Python: pysam + pybedtools for custom QC metrics.
  • Assess the quality of my ChIP-seq experiment" → Compute FRiP, cross-correlation (NSC/RSC), library complexity, and IDR replicate concordance to evaluate enrichment success. CLI: deeptools plotFingerprint, phantompeakqualtools run_spp.R Python: pysam + pybedtools for custom QC metrics.
  • Quality metrics for assessing ChIP-seq experiment success and replicate reproducibility.
  • reads_in_peaks=$(bedtools intersect -a chip.bam -b peaks.narrowPeak -u | samtools view -c -) total_reads=$(samtools view -c -F 260 chip.bam).

Source Doc

Excerpt From SKILL.md

FRiP (Fraction of Reads in Peaks)

Goal: Quantify enrichment strength by measuring the proportion of reads falling within called peaks.

Approach: Count reads overlapping peak regions and divide by total mapped reads.

Calculate FRiP

frip=$(echo "scale=4; $reads_in_peaks / $total_reads" | bc) echo "FRiP: $frip"


## Convert peaks to SAF format

awk 'BEGIN{OFS="\t"} {print $4, $1, $2, $3, "."}' peaks.narrowPeak > peaks.saf

Use cases

  • Use when assessing ChIP-seq data quality metrics.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • peak-calling - Call peaks before QC analysis
  • alignment-files - BAM statistics and filtering
  • differential-binding - Compare conditions after QC
  • atac-seq/atac-qc - Similar QC for ATAC-seq

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