atac-footprinting

What problem does it solve?

Analyzing transcription factor occupancy from ATAC-seq data is challenging due to biases and the need to infer binding from accessibility patterns. This skill provides an end-to-end footprinting workflow using TOBIAS to correct Tn5 bias, scan motifs, score footprints, and optionally perform differential footprinting across conditions.

Core Features & Use Cases

• Bias-corrected footprinting: Tn5 bias correction with ATACorrect to improve footprint accuracy.
• Motif scanning & scoring: Identify motif sites and compute footprint scores across samples.
• Differential footprinting: Compare TF occupancy between conditions and generate aggregated plots.
• Outputs & reports: Provides TF-binding calls and plots for interpretation in downstream analyses.

Quick Start

Run the ATACseq footprinting workflow by supplying ATAC-seq BAMs, peak files, a reference genome, and motif PWMs to generate footprint scores and TF binding reports.