How are on-target scores calculated?

On-target scores are calculated based on Doench, Fusi et al. 2016. Scores above 60 are considered to be good guides. Use these scores to rank guides relative to each other.

How are off-target scores calculated?

Off-target scores are calculated based on Hsu et al. 2013. If you have not provided a genome region, scores may differ from other sites (such as crispr.mit.edu). Scores range from 0-100, with higher being better. Off-target scores above 50 are considered to be good guides (see http://crispr.mit.edu/about#score). Use these scores to rank guides relative to each other.

Why are my paired nickase scores lower than my single guide scores?

We calculate paired nickase scores using the same calculations as crispr.mit.edu. Paired scores should be compared relative to other paired scores, while the single guide scores should be compared to other single guide scores. It is a bit unintuitive that the score is lower for the paired compared to single, considering that the nickase pair will have a lower off-target cut probability overall biologically.

Why can I only see a finite number of off-target sites? 

On the backend, we do search for all of the off-targets, but pare down the list to 49 for the ones we show you (in effect, showing you the top possible off-targets).

How do I set the genomic region of my imported sequence?

To set the genomic region for off-target score calculations, click on No region set to manually set the genomic location. To note, genomic indices are imported with the gene if you import the full sequence, but are removed if you import only cDNA.

How do I export a table of on or off-target scores and sites? 

To export a table of potential guides, chose the Save dropdown and export some or all of your guides. 

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