Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-atac-seq-footprinting

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-atac-seq-footprinting🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatindetect

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-atac-seq-footprinting

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: TOBIAS ATACorrect → TOBIAS FootprintScores → TOBIAS BINDetect.
Identify TF binding footprints in my ATAC-seq data" → Detect protected DNA regions within accessible chromatin where bound transcription factors block Tn5 insertion. CLI: TOBIAS ATACorrect → TOBIAS FootprintScores → TOBIAS BINDetect.
tobias ATACorrect \ --bam sample.bam \ --genome genome.fa \ --peaks peaks.bed \ --outdir corrected/ \ --cores 8.

Source Doc

Excerpt From SKILL.md

TOBIAS Workflow

Goal: Identify transcription factor binding footprints within accessible chromatin regions.

Approach: Correct Tn5 insertion bias, compute per-base footprint scores, then detect bound/unbound TF motif sites using the three-step TOBIAS pipeline.


## 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