# CLIP Motif Analysis - Usage Guide

> Find enriched sequence motifs at CLIP-seq binding sites to characterize RBP binding preferences.

- Skill: `tools-only/clip-motif-analysis-usage-guide` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add tools-only/clip-motif-analysis-usage-guide`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tools-only/clip-motif-analysis-usage-guide/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: tools-only (https://skillmd.com/u/tools-only)
- Updated: 2026-09-29
- Page: https://skillmd.com/skills/tools-only/clip-motif-analysis-usage-guide

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# CLIP Motif Analysis - Usage Guide

## Overview

Find enriched sequence motifs at CLIP-seq binding sites to characterize RBP binding preferences.

## Prerequisites

```bash
conda install -c bioconda homer meme bedtools
```

## Quick Start

- "Find de novo motifs at binding sites"
- "Check for known RBP motifs"

## Example Prompts

> "Run HOMER motif analysis on my CLIP peaks"

> "Find enriched 6-8mer motifs"

## What the Agent Will Do

1. Extract peak sequences (bedtools getfasta)
2. Run de novo motif discovery
3. Compare to known RBP motifs
4. Report enriched motifs

## Tips

- **Use -rna flag** for RNA motifs in HOMER
- **Background** should match GC content
- **6-8 nt motifs** are typical for RBPs