# Bio Clip Seq Clip Motif Analysis

> Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.

- Skill: `bg-szy/bio-clip-seq-clip-motif-analysis` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add bg-szy/bio-clip-seq-clip-motif-analysis`
- Raw SKILL.md: https://api.skillmd.com/api/skills/bg-szy/bio-clip-seq-clip-motif-analysis/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: bg-szy (https://skillmd.com/u/bg-szy)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/bg-szy/bio-clip-seq-clip-motif-analysis

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# CLIP Motif Analysis

## HOMER De Novo 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


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