created by [email protected] 08/08/2022
- Download files files from GEO (GSE211045)
- Git clone or download our files and scripts to your local/virtual environment.
- Modify config_scz.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 scz_file_foldername: to identify where the files from GEO are stored.
- Modify output_file_dir: to identify the location of the mpra result.
- Generate MPRA results:
- run generate_mpra_result_from_count_fastq if you want to generate MPRA results from FASTQ files
- 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).
- MPRA result will be created within the folder you specificied above (output_file_dir:).
Please cite this paper: McAfee JC*, Lee S*, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle BP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. (2023) Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants. Cell Genomics doi.org/10.1016/j.xgen.2023.100404.