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QuantNado

Call Peaks

Milne-Group/QuantNado

`call-peaks`¶

Call peaks directly from a QuantNado dataset.

Usage¶

quantnado call-peaks \
  --zarr dataset/combined.zarr \
  --output-dir peaks

Required Options¶

--zarr: path to a QuantNado store or a directory of per-sample stores
--output-dir: directory for output BED files

Methods¶

quantile: fast default method
seacr: SEACR-style peak calling with optional control store
lanceotron: ML-based peak calling, typically for ChIP-seq

Common Options¶

--method TEXT: quantile, seacr, or lanceotron
--assay TEXT: array key to call peaks on, such as atac or chip_h3k27ac
--blacklist PATH: BED file of excluded regions
--log-file PATH: log destination
--verbose, -v: debug logging

Quantile Options¶

--tilesize INTEGER
--window-overlap INTEGER
--quantile FLOAT
--merge / --no-merge

Example:

quantnado call-peaks \
  --zarr dataset \
  --method quantile \
  --assay atac \
  --quantile 0.98 \
  --output-dir peaks

SEACR Options¶

--control-zarr PATH
--fdr FLOAT
--norm TEXT
--stringency TEXT
--n-workers INTEGER
--device TEXT

Example:

quantnado call-peaks \
  --zarr chip_dataset \
  --method seacr \
  --assay chip_h3k27ac \
  --control-zarr igg_dataset \
  --output-dir peaks_seacr

LanceOTron Options¶

--score-threshold FLOAT
--smooth-window INTEGER
--batch-size INTEGER
--n-workers INTEGER
--device TEXT

Example:

quantnado call-peaks \
  --zarr chip_dataset \
  --method lanceotron \
  --assay chip_h3k27ac \
  --output-dir peaks_lanceotron

Output¶

QuantNado writes BED files to the requested output directory, one result per eligible sample.