As I am newbie to CRISPR/Cas9 techniquein bacteria, I wonder if anybody could help me with spacer design. I plan to work with pdCas9 plasmid and repress expression of gene of interest. Is there any software, which can be used to design spacers and check for off-target interaction?
E-CRISP: http://www.e-crisp.org/E-CRISP/
CHOPCHOP: http://chopchop.cbu.uib.no/
Cas-OFFinder: http://www.rgenome.net/cas-offinder/
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Not a CRISPR/Cas9 user.
I use Crispor: http://crispor.tefor.net/
It uses a similar guideseq algorithm and give you a very useful comparison with other algorithms (like the MIT crispr off-target predictor)
You can download the pipline (of crispor or guideseq) in github if you want a stand-alone version (you can add your own genomes!).
Greetings!
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