- Install the conda virutal environment for sgRNAcas9.
- Download the GUI version of sgRNAcas9 from SourceForge.
- Activate the sgRNAcas9 virtual environment.
- 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
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.