Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-chipseq-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

ChIP-seq: alignment → peak calling → motif analysis → annotation.

OpenClawNanoClawAnalysisReproductionbio-workflows-chipseq-pipeline🧠 bioos extended suitebioos extended bioinformatics suitechip

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow from raw ChIP-seq FASTQ files to annotated peaks.
for sample in IP_rep1 IP_rep2 Input_rep1 Input_rep2; do fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \ -o trimmed/${sample}_R1.fq.gz -O trimmed/${sample}_R2.fq.gz \ --detect_adapter_for_pe \ --qualified_quality_phred 20 \ --length_required 25 \ --html qc/${sample}_fastp.html done.

Source Doc

Excerpt From SKILL.md

Build index (once)

bowtie2-build genome.fa bt2_index/genome

Align

for sample in IP_rep1 IP_rep2 Input_rep1 Input_rep2; do bowtie2 -p 8 -x bt2_index/genome
-1 trimmed/${sample}_R1.fq.gz
-2 trimmed/${sample}_R2.fq.gz
--no-mixed --no-discordant
--maxins 1000
2> aligned/${sample}.log |
samtools view -@ 4 -bS -q 30 - |
samtools sort -@ 4 -o aligned/${sample}.bam done


**QC Checkpoint:** Check alignment rate
- Overall alignment >80%
- Unique mapping >70%

## Narrow peaks (TFs, sharp histone marks like H3K4me3)

macs3 callpeak \
    -t aligned/IP_rep1.final.bam aligned/IP_rep2.final.bam \
    -c aligned/Input_rep1.final.bam aligned/Input_rep2.final.bam \
    -f BAMPE \
    -g hs \
    -n experiment \
    --outdir peaks \
    -q 0.01

Use cases

Use bio-workflows-chipseq-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-chipseq-pipeline to sequencing, variant, or omics analysis tasks.