Need more help or want additional documentation?

See our github repo here.

Basic Usage Instructions:
1. Get gRNAs from desired design website in the correct format

FOR CHOPCHOP: Navigate to the CHOPCHOP gRNA design website and follow the instructions to get your gRNAs. Copy the contents of the gRNA results table (without the header) and paste them into the input field on the home page. If using gRNAs designed via a fasta sequence on chopchop, please enter the chromosome number being targeted on the first line of the input box, with the results table information on the lines that follow.

FOR CRISPR-ERA: Navigate to the CRISPR-ERA gRNA design website and follow the instructions to get your gRNAs. Copy the contents of the gRNA results table (without the header) and paste them into the input field on the home page.

FOR E-CRISP: Navigate to the E-CRISP gRNA design website and follow the instructions to get your gRNAs. Click "Download a tabular report" and paste

all

the contents of the file into the gRNA entry box. We'll get rid of the header for this one.

FOR USE MY OWN: Enter information in tab separated format with columns "Rank" "Sequence" "Chromosome" "BasePair". Then paste into gRNA input box and query.

2. Select your gRNA filtering method

There are three routes for filtering your gRNAs based on nucleosome occupancy utilizing two nucleosome maps (see ABOUT for more information):

1. filtering dynamically (recommended), which combines novel nucleosome data from two maps (unique and redundant) to re-rank nucleosomes based on both degree of nucleosome occupancy and spatial constraints.
2. doing a strict filter, which re-ranks gRNAs systematically based solely on overlap with nucleosomes disregarding occupancy score.
3. doing a lenient filter which only utilizes the unique nucleosome map to filter gRNAs.

3. Get your re-ranked gRNAs and get to experimenting!