call-footprints

Calculate a continuous footprint score from bias-corrected cut-site signal within accessible regions. Higher local depletion relative to flanking signal produces 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.

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.

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