Paired nickase analysis

[beatrizdslmartins]

Hello,

I am to use CRISPResso2 to to analyze indels in KO samples generated using the paired nickase strategy. Ideally, I would like to input two sgRNA sequences and analyze all the indels occurring in the region between and around them.

My goal is to compare the efficiency of:

• Each guide used separately with wtCas9
• Both guides used together with the paired nickase (D10A)

Could you please guide me on which settings I could adjust to ensure accurate analysis in this context? I would greatly appreciate any recommendations.

Thank you for your help!

[Colelyman]

Hi @beatrizdslmartins,

Sorry for the delay in response! In case you haven't already figured out how to analyze this with CRISPResso, here is how I would go about it. I would use CRISPRessoBatch to analyze and compare the efficiencies. In the batch file, you can supply multiple guides by separating them with a comma and CRISPResso will quantify edits at both loci.

I have attached an example batch file that you can base your analysis off of paired_nickase.txt. Then you can run it like this:

CRISPRessoBatch -bs paired_nickase.txt <add any other parameters that you would like to apply to all samples>

Please let us know if you have any additional questions or need any more help!

Best of luck,
Cole