/CRISPR-PACMAN-pool-generation

Primary LanguagePython

CRISPR-PACMAN guide design

1. Create a set of group-specific guide RNAs ("Horizontal pool")

Extract a comprehensive set of guide RNAs that target conserved regions of a fasta alignment file

python horizontal/horizontal.py aligned_sequences.fasta -o ./horizontal_pool_output

2. Create a family-spectrum crRNA set ("Minipool")

Generate a very small pool of guide RNAs that target all genomes in a fasta file

python minipool/prepare_guide_candidates.py sequences.fasta -o ./minipool_output
python minipool/set_cover.py -o ./minipool_output

3. Generate predicted scores for crRNAs

First, run the Cas13 Guide Design tool from the Sanjana lab (https://gitlab.com/sanjanalab/cas13/-/tree/master/Cas13designGuidePredictor) on your fasta reference sequence of interest to generate an output csv file. Then run the following script to generate a .json of scored guides

python score_guides.py -t scores.csv -o ./score_output/