bio-atac-seq-footprinting
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
npx skills add majiayu000/claude-skill-registry --skill footprinting --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.
# TF Footprinting ## TOBIAS Workflow ```bash # 1. Correct Tn5 bias tobias ATACorrect \ --bam sample.bam \ --genome genome.fa \ --peaks peaks.bed \ --outdir corrected/ \ --cores 8 # 2. Calculate footprint scores tobias FootprintScores \ --signal corrected/sample_corrected.bw \ --regions peaks.bed \ --output footprints.bw \ --cores 8 # 3. Bind TF motifs tobias BINDetect \ --motifs JASPAR_motifs.pfm \ --signals footprints.bw \ --genome genome.fa \ --peaks peaks.bed \ --outdir bindetect_output/ \ --cores 8 ``` ## TOBIAS Differential Footprinting ```bash # Compare conditions tobias BINDetect \ --motifs JASPAR_motifs.pfm \ --signals condition1.bw condition2.bw \ --genome genome.fa \ --peaks consensus_peaks.bed \ --outdir differential_footprints/ \ --cond_names condition1 condition2 \ --cores 8 # Output includes: # - Differential binding scores # - Per-TF statistics # - Bound/unbound site predictions ``` ## Download JASPAR Motifs ```bash # Download JASPAR motifs wget https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt mv JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt JASPAR_motifs.pfm ``` ## Prepare Input Files ```bash #
- TOBIAS Workflow
- TOBIAS Differential Footprinting
- Download JASPAR Motifs
- Prepare Input Files
- HINT-ATAC Alternative
- PIQ Footprinting
- Aggregate Footprint Plots
- Python: Custom Footprint Analysis
- Scan for Motifs
- Interpret Footprint Depth
- Quality Considerations
- Differential TF Activity
- TOBIAS Output Files
- Related Skills
tobias ATACorrect \ tobias FootprintScores \ tobias BINDetect \ Compare conditions Output includes: Download JASPAR motifs wget https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt mv JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt JASPAR_motifs.pfm Ensure BAM is sorted and indexed samtools sort -@ 8 sample.bam -o sample.sorted.bam
What does the bio-atac-seq-footprinting skill do?
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill footprinting --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.