Generating Sequencing Data

Note

The code (Seq_Sim/seq_sim.py and Seq_Sim/utils/seq_sim_utils.py) is based on R scripts from the Zhang Lab. These R scripts have been modified and streamlined for this project. The biological relevance may not be fully retained, and it serves as a showcase for potential sequencing simulations. For more information, please see Seq_Sim/README.md.

You can generate simulated sequencing data by running the following command:

/Seq_Sim/simulations.sh -c /Seq_Sim/config.yml

Alternatively, you can run:

python /Seq_Sim/seq_sim.py \
      --num_samples 30                   \ # num samples
      --fold_change 0.5                  \ # fold change between disease and healthy samples
      --config_file /Seq_Sim/config.yml    # configuration file

By default, the output CSV files will be saved in the SOM_Seq_Sim/data/ directory.