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sgRNA_design_scripts

NOTE. This script has been developed for the following publication:

The script compares and finds the sgRNA sequences with desired features combining CRISPR-ERA (Liu et al, 2015), Yeast CRISPRi (Smith et al, 2016), and CHOPCHOP (Labun et al, 2019). Script available also in the "sgRNA-Donor-Design_Script.pdf" file (with descriptions and dataframes embedded in the code).

Getting started:

  1. Install RMarkdown in RStudio. No need of pre-installing the other packages needed for the script as they will be installed automatically (if they are not already).
  2. Check the data organisation in the example file provided in the Input folder (Data_Example_Analysis.xlsx). Replicate in the same way an input file with the desired genes.
  3. Download the script and place it in the same folder of the file to be analysed. The excel file name should end with "Analysis" and should be a .xlsx file. Changes in the script can be made to import other file formats.
  4. Open the script and follow the directions. Make changes upon need (replace grouping variables, fluorescence analysis, dimentions of images, etc.).

Luca Torello Pianale, lucat@chalmers.se, Industrial Biotechnology Division, Chalmers University of technology

Created: December, 2023.

The scripts were tested with: R Version 4.3.0 (2023-04-21 ucrt) - RStudio (2021.09.2 Build 382)

Acknowledgment of support: This material is based upon work supported by the Novo Nordisk Foundation grant DISTINGUISHED INVESTIGATOR 2019 - Research within biotechnology-based synthesis & production (#0055044).