# Bio Chipseq Motif Analysis

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP.

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-motif-analysis -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-motif-analysis -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-motif-analysis -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-motif-analysis -g -a gemini-cli -y`

## Description

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: BioPython 1.83+, bedtools 2.31+, matplotlib 3.8+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- 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.

# Motif Analysis

**"Find enriched motifs in my ChIP-seq peaks"** → Discover de novo DNA-binding motifs and test for known TF motif enrichment in peak sequences.
- CLI: `findMotifsGenome.pl peaks.bed hg38 output/` (HOMER), `meme-chip -db JASPAR peaks.fa` (MEME)

Identify DNA sequence motifs enriched in ChIP-seq or ATAC-seq peaks to discover transcription factor binding sites.

## Tool Comparison

| Tool | Strengths | Use Case |
|------|-----------|----------|
| HOMER | Fast, comprehensive, built-in databases | General motif analysis |
| MEME-ChIP | Multiple algorithms, web interface | Publication-quality |
| MEME | De novo discovery only | Simple discovery |
| FIMO | Known motif scanning | Genome-wide scanning |

## HOMER

### Installation

```bash
conda install -c bioconda homer

# Configure genome (required once)
perl /path/to/homer/configureHomer.pl -install hg38
perl /path/to/homer/configureHomer.pl -install mm10
```

### De Novo Motif Discovery

**Goal:** Discover enriched DNA-binding motifs directly from ChIP-seq peak sequences.

**Approach:** Run findMotifsGenome.pl on a peak BED file with a specified fragment size, optionally providing background regions and target motif lengths.

```bash
# Basic motif finding
findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200

# With background regions
findMotifsGenome.pl peaks.bed hg38 output_dir/ -size 200 -bg background.bed

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-chipseq-motif-analysis/SKILL.md