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BI
bio-chipseq-qc
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-qc
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- CLI：deeptools plotFingerprint，phantompeakqualtools run_spp.R。
- Python：pysam + pybedtools ，用于 custom QC metrics。
- Assess quality of my ChIP-seq experiment" → Compute FRiP，cross-correlation (NSC/RSC)，库 complexity，、 IDR replicate concordance to evaluate enrichment success. CLI：deeptools plotFingerprint，phantompeakqualtools run_spp.R Python：pysam + pybedtools ，用于 custom QC metrics。
- Quality metrics ，用于 assessing ChIP-seq experiment success 、 replicate reproducibility。
- reads_in_peaks=$(bedtools intersect - chip.bam -b peaks.narrowPeak -u | samtools view -c -) total_reads=$(samtools view -c -F 260 chip.bam)。
原始文档
SKILL.md 摘录
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
适用场景
- 适合在assessing ChIP-seq data quality metrics时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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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