jaspar-motifs
Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif database, binding profile, PWM, position weight matrix, TF motif, motif enrichment, motif scanning, binding site prediction.
npx skills add majiayu000/claude-skill-registry --skill jaspar-motifs-ammawla-encode-toolkit --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Instructs to integrate JASPAR PWMs with ENCODE ChIP-seq peaks to validate TF binding targets, discover co-binding partners, and scan regulatory elements for TF binding potential.
How it works
Describes retrieving ENCODE ChIP-seq peaks, obtaining JASPAR motif profiles via REST API, and converting motifs into formats suitable for scanning (PFM, PWM, MEME). Provides concrete steps to extract peak sequences (using bedtools getfasta and summit-centered extraction), then perform motif scanning and enrichment (FIMO, HOMER, MEME-ChIP). Includes guidance for interpreting enrichment results and a workflow for multi-TF co-binding analysis. Includes example code blocks for API access, retrieving PFMs, and obtaining MEME format for FIMO. Covers variant-impact analysis and a multi-TF co-binding workflow with concrete commands and scripts.
When to use it
Triggered when investigating ENCODE TF ChIP-seq data with motif context, such as validating motifs in peaks, discovering co-binding motifs, interpreting enhancers, assessing variants, comparing tissues, or planning CRISPR validation.
What it can touch
Touchpoints include external tools and formats: REST API calls to jaspar.genereg.net (matrix endpoints, format options), FIMO, HOMER, MEME-ChIP, bedtools, and sequence extraction steps. Specific commands and file formats are named, including ctcf_motif.meme, peak_sequences.fa, fimo_output/, and etc.
Caveats
Outlines potential pitfalls: motif similarity causing false positives, arbitrary PWM thresholds, multiple profiles per TF, GC-content background effects, motif presence not guaranteeing binding, and species-specific motifs. Provides cautionary notes without asserting outcomes.
# Using JASPAR Transcription Factor Binding Profiles with ENCODE ChIP-seq Data Integrate JASPAR position weight matrices (PWMs) with ENCODE ChIP-seq peaks to validate TF binding targets, discover co-binding partners, and scan regulatory elements for TF binding potential. ## Scientific Rationale **The question**: "Does the expected TF binding motif appear in my ENCODE ChIP-seq peaks, and what other TF motifs are enriched?" ENCODE TF ChIP-seq experiments identify where a transcription factor binds in the genome, but the peak coordinates alone do not confirm direct DNA binding or reveal the binding sequence specificity. JASPAR provides curated position weight matrices (PWMs) — mathematical representations of TF binding preferences — that enable two critical analyses: 1. **Target validation**: If CTCF ChIP-seq peaks are enriched for the CTCF motif (JASPAR MA0139.1), the experiment worked correctly. If they are NOT enriched, something may be wrong with the antibody, crosslinking, or peak calling. 2. **Co-factor discovery**: Motif enrichment analysis in ChIP-seq peaks often reveals motifs for co-binding TFs that were not the ChIP target, uncovering regulatory complexes. ### What JASPAR P
- Scientific Rationale
- What JASPAR Provides
- The ENCODE-JASPAR Synergy
- Key Literature
- When to Use This Skill
- JASPAR REST API Reference
- Key Endpoints
- Common Matrix IDs for ENCODE TFs
- Step 1: Retrieve ENCODE ChIP-seq Peaks
- Step 2: Get JASPAR Motif Profiles
- Query by TF Name
- Get the Position Frequency Matrix (PFM)
- Get MEME Format (for FIMO Scanning)
- Step 3: Extract Peak Sequences
Download reference genome (if not available)
Extract sequences from ENCODE peak regions
Use summit +/- 100bp for narrow peaks (better motif enrichment)
awk 'BEGIN{OFS="\t"} {mid=int(($2+$3)/2); print $1, mid-100, mid+100, $4}' \
encode_peaks.bed > peak_summits_200bp.bed
bedtools getfasta \
narrowPeak summit is relative to peak start (column 10)
awk 'BEGIN{OFS="\t"} {summit=$2+$10; print $1, summit-100, summit+100, $4}' \
encode_narrowpeak.bed > summit_regions.bed
Scan peak sequences for CTCF motifWhat does the jaspar-motifs skill do?
Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif database, binding profile, PWM, position weight matrix, TF motif, motif enrichment, motif scanning, binding site prediction.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill jaspar-motifs-ammawla-encode-toolkit --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.