How are off-target scores calculated?

  • Updated

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.


Aggregated off-target scores

Potential off-target site scores

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:

  • Lower off-target site scores for each candidate's off-target site
  • Fewer number of candidate off-target sites in total

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