genomic-region-annotation-integration

Reconstruct the footprint scoring step that converts bias-corrected ATAC-seq signal into per-base footprint scores

Summary

This skill converts bias-corrected ATAC-seq insertion signal into footprint scores by measuring Tn5 insertion depletion patterns within accessible chromatin regions. It quantifies the magnitude of transcription factor binding footprints at base-pair resolution for downstream differential binding and visualization.

When to use

Apply this skill after bias-correcting ATAC-seq cutsite signal (via ATACorrect) when you have a bias-corrected bigWig file and need to compute per-position footprint scores within defined accessible regions (peaks, called footprints, or regulatory regions) to detect and quantify transcription factor occupancy through characteristic insertion depletion.

When NOT to use

• Input bigWig is uncorrected or not yet bias-corrected; use ATACorrect first.
• You have no defined accessible chromatin regions; define peaks or regulatory regions before scoring.
• The goal is only bulk chromatin accessibility quantification without transcription factor binding inference; standard peak calling and quantification suffices.

Inputs

• bias-corrected bigWig file (from ATACorrect)
• BED file of accessible genomic regions (ATAC-seq peaks or footprint regions)

Outputs

• footprint-score bigWig file (per-base footprint scores across input regions)

How to apply

Load the bias-corrected bigWig file (output from ATACorrect) and supply a BED file of accessible genomic regions where footprint scoring should occur. Use TOBIAS ScoreBigwig to measure signal depletion at each base within those regions, generating a bigWig output where each position reflects the magnitude of observed insertion depletion. The tool operates on the principle that protein-bound sites show visible depletion of Tn5 insertions, quantifying this depletion as a footprint score. Validate the output bigWig for correct format (valid header, coordinate ranges), non-zero score distributions, and consistency with input region boundaries.