atac-seq-footprint-scoring

ATAC-seq footprint scoring

Summary

Convert bias-corrected ATAC-seq signal into per-base footprint scores that quantify transcription factor binding through Tn5 insertion depletion patterns. This intermediate step bridges raw cutsite bias correction and downstream TF occupancy classification by measuring signal magnitude at each genomic position.

When to use

You have completed Tn5 insertion bias correction on ATAC-seq reads and now need to quantify footprint signal strength (signal depletion around TF-bound sites) across accessible chromatin regions before classifying individual TF binding sites. Use this skill when your input is a bias-corrected bigWig file and a set of genomic intervals (peaks, footprint regions, or open chromatin windows) and your goal is to generate position-specific footprint magnitude scores.

When NOT to use

• Input BAM/cutsite data has not been bias-corrected for Tn5 sequence preferences — run TOBIAS ATACorrect first
• Input regions are not open chromatin or accessible regions — ScoreBigwig requires regions with measurable ATAC-seq signal
• Goal is to classify individual TF binding sites as bound/unbound — that requires downstream motif matching and BINDetect, not scoring alone

Inputs

• Bias-corrected bigWig file (from TOBIAS ATACorrect; e.g., *_corrected.bw)
• Genomic intervals in BED format (accessible chromatin peaks, footprint regions, or regulatory regions)

Outputs

• Footprint scores bigWig file (per-base signal depletion magnitude across input regions)
• Optional: footprint score summary statistics (mean, median, distribution across regions)

How to apply

Load the bias-corrected bigWig file (output from TOBIAS ATACorrect) and a corresponding set of accessible genomic regions in BED format. Apply TOBIAS ScoreBigwig, which computes footprint scores by measuring signal depletion magnitude within each region, generating a bigWig output where each genomic position reflects the observed insertion depletion pattern intensity. The tool integrates the corrected signal across the region and assigns scores that represent the magnitude of the footprint signal. Validate the output bigWig file for correct format (chromatin regions present, valid score distributions), non-empty signal coverage, and absence of NaN or infinite values before passing to downstream motif-based TF binding classification.