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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