Design CRISPR guides

The CRISPR Guide Designer scores SpCas9 guides on your plasmid. It also designs pooled guide sets across many targets.

Design knockout guides

1. Open the plasmid. Press Ctrl/Cmd+K and run CRISPR Guide Designer.
2. Under Design mode, choose Knockout.
3. Pick a Nuclease / PAM: SpCas9 (NGG) or SpCas9 (NAG).
4. Optionally pick a Cloning Vector to get cloning oligos for each guide.
5. Click Design Guides.
6. Tick Only guides in my selection to keep guides inside a selected region or feature.
7. Click Save to keep the guides in your library, or Download CSV.

Find base-editing guides

1. Under Design mode, choose Base edit.
2. Enter the Target position of the base to change.
3. Choose the Intended change: A to G (ABE) or C to T (CBE).
4. Leave Editor on Auto to see all compatible editors, or pick one.
5. Click Find guides. Each guide shows its editing window and any bystander bases.

Design a pooled or tiled set

1. Click Batch / pool.
2. Enter a Pool name and set Guides / target.
3. Choose Nuclease / PAM and Cloning vector.
4. Tick Tile guides across each target to spread guides along each target instead of ranking the best.
5. Add targets, each with a unique name and pasted DNA.
6. Click Design pooled guides, then Plate order CSV.

Import a guide library

1. In single-target mode, click Import library from file....
2. Choose a CSV or TSV with a sequence column, or a FASTA file.
3. Review the imported and rejected rows. Click Download rejected as CSV to fix them in the source file.
4. Click Add N guides to project.