examples

Example Usage Scripts

This directory contains example scripts demonstrating common use cases for the UMI RNA Simulator.

Available Examples

basic_usage.py

Common simulation scenarios with synthetic data:

• Basic simulation with default parameters
• High PCR amplification
• Target read count mode
• Paired-end sequencing

Run it:

python examples/basic_usage.py

advanced_usage.py

Advanced features using real genomic data:

• Bacterial genome simulation (CP003773)
• Mouse chromosome 19 simulation
• Custom sequencing parameters
• UMI inline sequence mode

Run it:

python examples/advanced_usage.py

Output

All examples create an output/ directory with simulation results:

• FASTQ files (.fastq.gz)
• Statistics files (_stats.txt)
• Ground truth files (_truth.txt)

Modifying Examples

Feel free to copy and modify these scripts for your own needs. Common modifications:

Change output directory:

sim.run_simulation(output_prefix="my_custom_output/sim")

Adjust molecule counts:

sim = BulkRNAUMISimulator(
    n_genes=500,
    total_molecules=100000,  # More molecules
    ...
)

Different PCR conditions:

sim = BulkRNAUMISimulator(
    pcr_cycles=15,        # More cycles
    pcr_efficiency=0.85,  # Higher efficiency
    ...
)

See Also

• Quick Start Guide
• Installation Guide
• Main README