---
name: bio-clip-seq-clip-motif-analysis
source: https://app.decimal.ai/s/bio-clip-seq-clip-motif-analysis@2/SKILL.md
source_sha256: 4f4b84375a18
---

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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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