tf-footprint-differential-analysis

Differential transcription factor occupancy from ATAC-seq data is identified by running TOBIAS ATACorrect and ScoreBigwig on pseudobulk BAM files to quantify and compare TF footprints across conditions like WT versus KO.

Validating open-chromatin signals requires measuring actual TF binding across treated versus control conditions. This is achieved by running pseudobulk ATAC-seq differential binding analyses to detect changes in TF occupancy at regulatory regions.

Yes, you can use HINT-ATAC or Signac Footprint() for footprint visualization to corroborate occupancy findings. These serve as optional visualization steps alongside the core TOBIAS ATACorrect, ScoreBigwig, and BINDetect differential binding workflow.

Yes, you need pseudobulk ATAC-seq BAM files to run differential TF footprinting analysis. The workflow compares conditions such as treated versus control by applying TOBIAS tools to these aggregated BAM files to validate TF occupancy at regulatory regions.

The TOBIAS BINDetect workflow outputs occupancy-focused reports quantifying differential TF binding across compared conditions. It processes ATAC footprints to validate regulatory TF occupancy changes between samples like WT and KO.