Closed ytakemon closed 3 years ago
Hi Yuka,
Thanks for the interest, unfortunately this tool does not currently offer a streamlined way to check specific user-generated sgRNA. One could probably approximate this by loading the Rule_Set_2_Model
inside this package and running:
processed_sgRNA <- Doench_2016_processing(sgRNA_list)
efficiency_score <- stats::predict(Rule_Set_2_Model, processed_sgRNA, n.trees = 500)
The sgRNA_list
is your sgRNA as a list of strings. This function is not designed to be called by the user, so there are a few things to note - namely that the nucleotides that compose the sgRNA in sgRNA_list need to be DNA bases ('T' instead of 'U'), and that the sgRNA must include flanking sequence on either side of guide (30-mer, four bases before the start and three bases after the PAM).
Best, Dylan
I'll give that a try. Thanks, Dylan!
Hello,
I was wondering if I can use your tool to calculate the on- and off-target scores of sgRNAs that I have instead of those that are selected by this tool. For example, I have a screen that used the Gecko V2 sgRNA library, and I would like to know which guides might have lower efficiency scores (as determined by the on- & off- target scores).
Thank you, Yuka