call-footprints

Calculate a footprint score at each position in accessible regions using the corrected bigWigs from atac-correct. The score measures local cut-site depletion relative to the surrounding signal; higher scores indicate stronger footprint evidence.

Example command

call-footprints \
  --signals A_corrected.bw B_corrected.bw \
  --sample-names A B \
  --regions merged_peaks.bed \
  --sample-output-root project/samples

Primary inputs

• --signals — one bias-corrected cut-site signal bigWig per sample.
• --sample-names — labels in the same order as --signals.
• --regions — BED intervals in which scores are calculated; normally the project merged, filtered peaks.
• --sample-output-root — root represented by {sample_root} below.

Replace A_corrected.bw and B_corrected.bw with your corrected tracks. In a project, these are under project/samples/{sample}/atac_correct/; use project/peaks/merged_peaks_filtered.bed for the regions.

Main outputs

Path	Meaning
{sample_root}/{sample}/footprints/{sample}_footprints.bw	Base-resolution footprint score bigWig used by match-motifs and diff-footprints.
{sample_root}/{sample}/footprints/{sample}_candidate_footprints.bed	Optional local score maxima for de novo motif discovery; written with --call-candidates.
user-selected *.npz	Optional compressed scale-by-position score arrays when --score multiscale is used with an NPZ output option.

In direct mode, --output result.bw writes exactly result.bw; multiple signals written through --outdir {outdir} use {outdir}/{signal_stem}_footprints.bw.

Pass the footprint score tracks to match-motifs to summarize evidence at known motif sites. Keep the corrected cut-site tracks for aggregate plots, which show the signal shape around those sites.

Continue with match-motifs, or see the complete call-footprints reference.