/bio-clip-seq-clip-motif-analysis
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$ npx -y skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clip-seq-clip-motif-analysis --agent claude-codeHow it fires
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/bio-clip-seq-clip-motif-analysis
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SKILL.md
bio-clip-seq-clip-motif-analysis.SKILL.md<!--
COPYRIGHT NOTICE
This file is part of the "Universal Biomedical Skills" project.
Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
All Rights Reserved.
#
This code is proprietary and confidential.
Unauthorized copying of this file, via any medium is strictly prohibited.
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Provenance: Authenticated by MD BABU MIA
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--- 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 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:
- read_file
- run_shell_command
---
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 \
-rnaMEME-ChIP
meme-chip -oc output_dir \
-dna \
peaks.faKnown Motif Enrichment
# HOMER known motif scan
findMotifs.pl peaks.fa fasta output_dir \
-rna \
-knownRelated Skills
- clip-peak-calling - Get peaks
- chip-seq/motif-analysis - General motif concepts
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