README for cross-disorder MPRA

BEFORE RUNNING SCRIPTS

1. Download files files from GEO (GSE244011)
2. Git clone or download our files and scripts to your local/virtual environment.
3. Modify config_CD.yml file within files/ folder (You only need to modify first three variables).
   • Modify script_dir: to identify where the scripts/ from github are stored.
   • Modify cd_file_foldername: to identify where the files from GEO are stored.
   • Modify output_file_dir: to identify the location of the mpra result.
4. Modify where_the_config_file_is_stored in the first line of code for generate_mpra_result_from_count_matrix to identify the location of your config file

RUNNING SCRIPTS

1. Generate MPRA results:
   • run generate_mpra_result_from_count_matrix if you want to generate MPRA results from DNA/RNA count files (these files are preprocessed, merged, and modified FASTQ files).
2. MPRA result will be created within the folder you specificied above (output_file_dir:).

REFERENCE

Please cite this paper: Lee et al., Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders. (2025) Cell doi: 10.1016/j.cell.2024.12.022.