AgentSkillsCN

bio-clip-seq-clip-motif-analysis

在 CLIP-seq 结合位点中识别富集的序列基序，以明确 RBP 结合的特异性。在表征 RNA 结合蛋白的序列偏好时，可选用此功能。

SKILL.md
--- frontmatter
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

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