bio-clip-seq-clip-motif-analysis
$
npx mdskill add GPTomics/bioSkills/bio-clip-seq-clip-motif-analysisDiscover enriched RNA motifs at CLIP-seq peaks to define RBP specificity.
- Identifies overrepresented sequence patterns in RNA-binding protein binding sites.
- Depends on HOMER, bedtools, and MEME-ChIP for motif discovery.
- Selects motif lengths and RNA mode based on input peak coordinates.
- Outputs enriched motif sequences and statistical significance metrics.
SKILL.md
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---
name: bio-clip-seq-clip-motif-analysis
description: Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
tool_type: cli
primary_tool: HOMER
---
## Version Compatibility
Reference examples tested with: bedtools 2.31+
Before using code patterns, verify installed versions match. If versions differ:
- 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.
# CLIP Motif Analysis
**"Find sequence motifs at my RBP binding sites"** → Discover enriched RNA sequence motifs at CLIP-seq peaks to determine the binding specificity of an RNA-binding protein.
- CLI: `findMotifs.pl peaks.fa fasta output/ -rna` (HOMER)
- CLI: `bedtools getfasta` to extract peak sequences first
## HOMER De Novo Motifs
**Goal:** Discover enriched RNA sequence motifs at CLIP-seq binding sites.
**Approach:** Extract FASTA sequences from peak regions using bedtools getfasta, then run HOMER findMotifs.pl in RNA mode to identify overrepresented motifs.
```bash
# Extract sequences from peaks
bedtools getfasta -fi genome.fa -bed peaks.bed -fo peaks.fa
# Find enriched motifs
findMotifs.pl peaks.fa fasta output_dir \
-len 6,7,8 \
-rna
```
## MEME-ChIP
```bash
meme-chip -oc output_dir \
-dna \
peaks.fa
```
## Known Motif Enrichment
```bash
# HOMER known motif scan
findMotifs.pl peaks.fa fasta output_dir \
-rna \
-known
```
## Related Skills
- clip-peak-calling - Get peaks
- chip-seq/motif-analysis - General motif concepts