When analyzing gRNAs, Benchling calculates two types of scores associated with off-target assessment:
- Aggregated off-target score
- Potential off-target site score
The meaning of the score depends on which off-target score you're referencing.
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Aggregated off-target scores |
Potential off-target site scores |
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| Definition | Each gRNA has one aggregated off-target score. The aggregation scoring approach is described in Hsu et al. 2013, but was also applied for the Doench method to provide a uniform set of scores. | Benchling numbers and scores all potential off-target sites in selected genomes. This means each gRNA can have multiple potential off-target sites, each with their own score. |
| How to view | In the list of gRNA in the Design CRISPR tab | In the pop-up window after clicking into each gRNA’s aggregate off-target score |
| Meaning | Higher aggregated off-target scores are generally better guides. |
High scoring off-target sites indicate a high likelihood the gRNA will interact with that off-target site, which is generally not wanted. In general, A “good” gRNA with the highest aggregate off-target score should have either or both:
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