bio-clip-seq-clip-motif-analysis

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

# 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

meme-chip -oc output_dir \
    -dna \
    peaks.fa

Known Motif Enrichment

# 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