ChromatinAccessibilityEngine: ATAC-seq Peak Calling, Nucleosome Positioning, and Transcription Factor Footprinting
Chromatin accessibility measured by ATAC-seq reveals the regulatory landscape of the genome, identifying active enhancers, promoters, and transcription factor binding sites. We present ChromatinAccessibilityEngine, a pure-Python pipeline for ATAC-seq analysis. The engine implements peak calling (CPM-normalized Poisson test, BH FDR), nucleosome-free region (NFR) vs nucleosomal fragment classification, transcription factor footprinting (Tn5 insertion bias correction, protection score), differential accessibility analysis, and motif enrichment at peaks. Applied to 20 samples × 100,000 genomic bins, the pipeline identifies 15,143 peaks, 45% NFR fragments, 5000 differential peaks (FDR<0.05), FRiP=0.565, and 50 enriched TF motifs.
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
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