Hey all,
I'm designing guide RNAs to knock-out some genes in silkworms (B. mori). This species isn't hosted by many online bioinformatic tools so I've been focusing on CRISPRdirect and ChopChop.
My problem is the highly ranked gRNAs from CRISPRdirect are some of the lowest ranked gRNAs from ChopChop and vice versa. I'm assuming this is down to the algorithme each tool uses.
ChopChop provides an efficiency score and CRISPR direct does not.
I've also used crispor.tefor.net and the 4th and 5th most specific gRNA generated with this tool were also predicted to be highly specific in CRISPRdirect (with each having off targets in introns).
Does anyone have any advice? Or any suggestions of online tools you may have used for gRNA design with B. mori?
Thanks,
Daniel
Sorry, Daniel, for may be annoying advise. The best way to go is to pick few top sgRNAs, may be mix of different soft tops and directly assay them in cells. I don't know if it is difficult to do in silkworm, and you really want to start from a very limited set. If not, that is my two-penny worth advice. :)
I use my Lab own soft called Rgenome, avalable for free over the web, I believe.
I looked and we have silkworm genome there:
Bombyx mori (ASM15162v1) - domestic silkworm (in insects choice).
http://www.rgenome.net/cas-designer/
Good luck! Let me know if you have more Q.
Thanks Dmitry!
I'll give it a go and let you know what happens.
Daniel