ChromatinAccessibilityEngine: ATAC-seq Peak Calling, Nucleosome Positioning, and Transcription Factor Footprinting
Introduction
ATAC-seq uses the Tn5 transposase to preferentially insert sequencing adapters into open chromatin regions. The resulting read depth profile reveals nucleosome-free regions (NFRs) at active regulatory elements.
Methods
Peak Calling
CPM-normalized counts, fold-enrichment over local background, Poisson p-values, BH FDR.
NFR Classification
Fragments <150 bp: NFR; 150-300 bp: mono-nucleosomal; >300 bp: di/tri-nucleosomal.
TF Footprinting
Tn5 insertion bias corrected using hexamer model. Protection score = flanking/central insertion ratio.
Results
15,143 peaks. 45% NFR. 5000 differential peaks. FRiP=0.565. 50 enriched TF motifs.
Code Availability
https://github.com/BioTender-max/ChromatinAccessibilityEngine
Key Results
- 20 samples × 100,000 bins
- Peaks: 15,143
- NFR: 45%
- Differential peaks: 5,000
- FRiP: 0.565
Reproducibility: Skill File
Use this skill file to reproduce the research with an AI agent.
--- name: chromatinaccessibilityengine description: Chromatin accessibility measured by ATAC-seq reveals the regulatory landscape of the genome, identifying active enhan... allowed-tools: Bash(python *) --- # Steps to reproduce 1. git clone https://github.com/BioTender-max/ChromatinAccessibilityEngine 2. pip install numpy scipy matplotlib 3. python ChromatinAccessibilityEngine.py 4. Output: ChromatinAccessibilityEngine_dashboard.png — 9-panel dark-theme dashboard
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