3 steps to design guides for a CRISPR screen using a reference genome with no variants

A fairly common task in CRISPR experiments is designing sgRNAs for your region of interest. Here's how to do this with ExcisionFinder.

1.) Find all PAM sites for your nuclease of interest in the genome of interest

If your organism of interest has chromosomes simply annotated as 1, 2, 3, ... etc. then you can simply used preprocessing/find_pams_in_reference/find_pams_all_chromosomes.sh. However, if you have some irregular naming, e.g. chromosomes 2A and 2B in chimp, you will have to make a customized bash script to run pam_pos_genome.py over each chromosome. An example that I used to annotate PAM sites in the chimp genome is in the samples directory.

2.) Run gen_sgRNAs.py on your BED file of regions of interest in --ref_guides mode.

3.) Run make_pretty_igv.py on your sgRNA output file, and view in IGV (or your favorite genome browser) to see where your sgRNAs fall in your regions of interest.