bio-workflows-chipseq-pipeline
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.
npx skills add BioTender-max/awesome-bio-agent-skills --skill chipseq-pipeline --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+, HOMER 4.11+, bedtools 2.31+, fastp 0.23+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - 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. # ChIP-seq Pipeline **"Process my ChIP-seq data from FASTQ to annotated peaks"** → Orchestrate QC, Bowtie2 alignment, duplicate removal, MACS3 peak calling, ChIPseeker annotation, and QC metrics (FRiP, strand cross-correlation). Complete workflow from raw ChIP-seq FASTQ files to annotated peaks. ## Workflow Overview ``` FASTQ files (IP + Input) | v [1. QC & Trimming] -----> fastp | v [2. Alignment] ---------> Bowtie2 | v [3. BAM Processing] ----> sort, markdup, filter | v [4. Peak Calling] ------> MACS3 | v [5. QC] ----------------> FRiP, fingerprint plots | v [6. Annotation] --------> ChIPseeker | v Annotated peaks + QC report ``` ## Primary Path: Bowtie2 + MACS3 + ChIPs
- Version Compatibility
- Workflow Overview
- Primary Path: Bowtie2 + MACS3 + ChIPseeker
- Step 1: Quality Control with fastp
- Step 2: Alignment with Bowtie2
- Step 3: BAM Processing
- Step 4: Peak Calling with MACS3
- Step 5: QC Metrics
- Step 6: Peak Annotation
- Parameter Recommendations
- Troubleshooting
- Complete Pipeline Script
- Related Skills
Process both IP and Input samples
for sample in IP_rep1 IP_rep2 Input_rep1 Input_rep2; do
fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \
done
Build index (once)
bowtie2-build genome.fa bt2_index/genome
Align
bowtie2 -p 8 -x bt2_index/genome \
samtools view -@ 4 -bS -q 30 - | \
samtools sort -@ 4 -o aligned/${sample}.bamWhat does the bio-workflows-chipseq-pipeline skill do?
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill chipseq-pipeline --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.