snp-crispr-hdr

Make sure you include full file paths for all scripts below.

snp-crispr-hdr.py ---------------

Given a list of SNPs, determines which pass the CRISPR system constraints for HDR (homology-directed repair).

Command to run:

python3 snp-crispr-hdr.py your_mpra_input.csv your_hdr_output.csv

crispr-motifbreakR.py ---------------

Given the output from the snp-crispr-hdr.py script and output from motifbreakR script (to be finalized), annotate your snps with motifbreakR data.

Command to run:

python3 crispr-motifbreakR.py your_motifbreakR_input.csv your_snp-crispr-hdr_input your_crispr-motifbreakR_output.csv

TODO: ---------------

Figure out how to nicely format headings on this markdown sheet

Upload a clean motifbreakR script

Later on: enable this pipeline to generate the motifbreakR file without the user having to generate their own.