quantnado 0.2.5

Quantile-based peak calling from RPKM bigWig files

QuantNado

quantnado-call-peaks is a quantile-based peak caller for CUT&Tag or ChIP-seq RPKM-scaled bigWig files. It tiles the genome, extracts log1p-transformed signal, and outputs BED files of high-signal regions using quantile thresholding.

quantnado-make-dataset generates an .h5ad (AnnData) file representing signal matrices across defined regions, using signal from multiple bigWigs.

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📦 Installation

Install from PyPI:

pip install quantnado

Requires Python ≥ 3.8

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🚀 Usage

🔹 Call Peaks

quantnado-call-peaks \
  --bigwig-dir path/to/bigwigs/ \
  --output-dir path/to/output/ \
  --chromsizes path/to/hg38.chrom.sizes \
  --tilesize 128 \
  --quantile 0.98 \
  --merge \
  --blacklist path/to/hg38-blacklist.bed \
  --tmp-dir tmp/

This will:

• Tile the genome in 128bp bins
• Extract log1p(RPKM) signal from each bigWig file
• Threshold each track at the 98th percentile (default)
• Output BED files of high-signal bins per track

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🔹 Make Dataset

quantnado-make-dataset \
  --bigwig-dir path/to/bigwigs/ \
  --output-file dataset.h5ad \
  --chromsizes path/to/hg38.chrom.sizes \
  --regions promoters_1024bp.bed \
  --blacklist hg38-blacklist.bed

If --regions is not provided, the genome will be tiled using --binsize (default: 128 bp).

The resulting .h5ad will contain:

• .X: matrix of mean RPKM per region per bigwig
• .obs: region metadata (chrom, start, end)
• .var: track names (from bigWig filenames)

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⚙️ Options

Option	Description
--bigwig-dir	Folder with .bw or .bigWig files
--chromsizes	Tab-separated chrom.sizes file (chr\tlength)
--blacklist	BED file of regions to exclude
--tilesize	Genomic bin size for peak calling (default: 128 bp)
--quantile	Quantile threshold for peaks (default: 0.98)
--merge	Merge adjacent bins into broader peaks
--regions	BED file of regions to extract signal over
--binsize	Bin size used if --regions is not specified (default: 128)
--output-file	Path to save .h5ad or .h5mu

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📁 Output Files

Peak caller (quantnado-call-peaks)

• *.bed: BED files of peaks for each bigwig

Dataset maker (quantnado-make-dataset)

• .h5ad: AnnData file with signal matrix