Bio Chipseq Motif Analysis
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP.
Install
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-motif-analysis -g -a claude-code -y- Repository
- FreedomIntelligence/OpenClaw-Medical-Skills3.1k
- Category
- Engineering
- Updated
- 4mo ago
- License
- See repository
- Context cost
- Mediumabout 2,532 tokens
- Runs scripts
- Yes, review before use
What it does
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.
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>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto 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
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.
# 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
