Version Compatibility

Reference examples tested with: bedtools 2.31+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

CLIP Motif Analysis

"Find sequence motifs at my RBP binding sites" → Discover enriched RNA sequence motifs at CLIP-seq peaks to determine the binding specificity of an RNA-binding protein.

• CLI: findMotifs.pl peaks.fa fasta output/ -rna (HOMER)
• CLI: bedtools getfasta to extract peak sequences first

HOMER De Novo Motifs

Goal: Discover enriched RNA sequence motifs at CLIP-seq binding sites.

Approach: Extract FASTA sequences from peak regions using bedtools getfasta, then run HOMER findMotifs.pl in RNA mode to identify overrepresented 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