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normalize-bigwig

Scale corrected cut-site signals using statistics measured over the same background regions. Use this optional step when samples require an explicitly shared signal scale before downstream scoring or plotting.

Example command

normalize-bigwig --sample-table project/metadata/samples.tsv --background project/peaks/merged_peaks_filtered.bed \
  --outdir project --method background-scale --stat q95 --target median

Primary inputs

  • --sample-table — project samples whose {sample}_corrected.bw files are normalized together.
  • --background — shared BED intervals used to calculate comparable background statistics.
  • --outdir — project directory represented by {project} below.
  • --method — transformation; background-scale multiplies each signal by a shared-target scale factor.
  • --stat — within-sample background statistic; the example uses the 95th percentile.
  • --target — across-sample target for the selected statistic; the example uses the median.

Main outputs

Path Meaning
{project}/samples/{sample}/normalize/{sample}_corrected_q95_scaled.bw Q95-scaled bias-corrected cut-site signal bigWig for one sample.
{project}/logs/normalize_q95/normalize_bigwig_qc.tsv Background statistics, selected statistic, target, and scale factor for every sample.
{project}/logs/normalize_q95/normalize_bigwig_manifest.tsv Sample-to-input/output signal mapping for downstream use.

In custom layout, default outputs use {outdir}/{input_stem}.background_scale_{stat}.bw, plus the two QC tables in {outdir}. background-zscore instead writes standardized signal and uses a method-specific filename suffix.

Download a representative ENCODE normalization QC table. See the Bulk ATAC-seq workflow and the complete normalize-bigwig reference.