Bio clip seq clip motif analysis
Skill FridrichMethod/awesome-skills/skills/bio-clip-seq-clip-motif-analysis
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.From its SKILL.md
npx -y skills add FridrichMethod/awesome-skills --skill bio-clip-seq-clip-motif-analysisAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
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SKILL.md
1.3 KB, 291 tokens by cl100k_base, as published. Nobody here has run it
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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
What ships with it: 2 files
1.5 KB alongside SKILL.md, 1 of them executable
examples/
- find_motifs.shruns440 B
- usage-guide.md1.1 KB