Published August 2, 2023
| Version v1
Journal article
Open
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variant
Creators
- 1. UNC
- 2. UCLA
- 3. University of Michigan
- 4. Harvard Medical School
- 5. Human Technopole
Description
README for SCZ MPRA
created by sool_lee@unc.edu 08/07/2023
BEFORE RUNNING SCRIPTS
- 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.
RUNNING SCRIPTS
- 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:)