search

dylanbeeber / crispRdesignR

Software used to design guide RNA sequences for CRISPR/Cas9 genome editing
13 stars 8 forks source link

Calculating on- and off-target scores of my own sgRNA #4

Closed ytakemon closed 3 years ago

ytakemon commented 3 years ago

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

dylanbeeber commented 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

ytakemon commented 3 years ago

I'll give that a try. Thanks, Dylan!