Command-Line Interface

QuantNado provides command-line tools for common workflows, accessible via the main quantnado command.

Overview

All QuantNado operations can be performed from the terminal without writing Python code:

quantnado --help

Available Commands

QuantNado provides the following commands:

Command	Purpose	Use Case
create-dataset	Convert BAM files to Zarr	Initial data processing
call-peaks	Call peaks from bigWig files	Peak identification

General Options

All commands support these options:

• --help, -h - Show command help and usage
• --verbose, -v - Enable debug logging
• --log-file - Path to save logs

Examples

Quick Start: Create Dataset

quantnado create-dataset sample1.bam sample2.bam \
  --output dataset.zarr \
  --chromsizes hg38.chrom.sizes

Quick Start: Call Peaks

quantnado call-peaks \
  --bigwig-dir ./bigwigs/ \
  --output-dir ./peaks/ \
  --chromsizes hg38.chrom.sizes \
  --quantile 0.98

Getting Help

Get help for any command:

quantnado --help                    # Main help
quantnado create-dataset --help     # Create dataset help
quantnado call-peaks --help         # Peak calling help

Current Limitations

• BAM file input requires local filesystem access
• Zarr output can be written to local or remote storage
• Large datasets may require significant disk space (see Storage Requirements)

See Also

• Create Dataset Command
• Call Peaks Command
• Python API
• Basic Usage