Bio clip seq clip motif analysis
Skill bg-szy/TOP-SKILLS/skills/awesome-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 bg-szy/TOP-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
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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: 1 file
1.1 KB alongside SKILL.md
- usage-guide.md1.1 KB