ATAC-seq Footprint Analysis using TOBIAS

1. Overview

This skill performs TF footprint detection and optional differential TF binding analysis using TOBIAS. It identifies true TF occupancy by modeling depletion of Tn5 insertions at motif cores.

Main steps include:

• Refer to the Inputs & Outputs section to check required inputs and set up the output directory structure.
• Always prompt user for genome assembly used.
• Always prompt user if other required files are missing.
• Tn5 bias correction with ATACorrect.
• Motif scanning.
• Footprint scoring.
• Binding detection with BINDetect.
• Aggregate footprint visualization.

2. When to use this skill