quantnado 0.1.4.dev0

Quantile-based peak calling from RPKM bigWig files

QuantNado

QuantNado is a quantile-based peak caller for CUT&Tag RPKM-scaled bigWig files. It tiles the genome, extracts log1p-transformed signal, and outputs BED files of high-signal regions using quantile thresholding. It also outputs log RPKM as a parquet file

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📦 Installation

Install using pip:

pip install quantnado

🚀 Usage

QuantNado \
  --bigwig path/to/file.bw \
  --output-dir path/to/output/ \
  --chromsizes path/to/hg38.chrom.sizes \
  # Optional parameters:
  --blacklist path/to/hg38-blacklist.bed \
  --tilesize 128 \
  --quantile 0.98 \
  --tmp-dir path/to/temp