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sgRNAcas9 is a package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites.

Running sgRNAcas9

  1. Install the conda virutal environment for sgRNAcas9.
  2. Download the GUI version of sgRNAcas9 from SourceForge.
  3. Activate the sgRNAcas9 virtual environment.
  4. In the directory for sgRNAcas9, run the following command to launch the sgRNAcas9 graphical user interface (GUI):
(sgRNAcas9) ~/sgRNAcas9_V3.0_GUI$ java -jar sgRNAcas9.jar

Using sgRNAcas9

In the sgRNAcas9 GUI…

  • Select the FASTA nucleic acid file of the target sequences in the “Target sequences(FASTA):” dialog box.
  • Select the FASTA nucleic acid file of the genome you want to design the guide RNAs for in the “Genome sequence(FASTA):” dialog box.
  • Click “RUN” to run the program

sgRNAcas9 will create a report directory in the current working directory. This directory contains its results. The most important file in this directory is sgRNAcas9_report.xls. This Excel files contains reported guide RNA sequences for CRISPR with quality score, and counts of potential off-target sites.