Frequently asked questions
- What Cas molecules is this tool appropriate for?
Our spacer design tool is appropriate for Cas molecules recognizing TTTR PAMs such as dCasMINI (Xu et al., 2021).
- What is the difference between activation and suppression guides?
Activation guides are located -1000bp/+200bp from the TSS and suppression guides are located -200bp/+1000bp from the TSS.
- How are off-targets computed?
20bp spacer sequences were sensitively mapped genome-wide using bowtie2 and then restricted to off-target sites containing TTTR within 5bp upstream of the spacer sequence (thus allowing for a single bp bulge). Final on-target spacer lists were sorted based on number of putative off-targets.
- What can I do if the a target gene I'm interested in doesn't appear?
We are always looking to expand the utility of this tool. We welcome any feedback regarding gene targets the community would find useful.
- Why do you never see any off-target count values above 5000 for any given on-target result?
On-target results with associated off-target values above 5000 exist. We simply don't report them.
- Is this tool capable of designing guides against genomes other than human?
While we currently only support guide design against the human genome (hg38), stay tuned as we plan to add additional genomes in the future to facilitate studies in model systems.
- Do you support guide design against additional PAMs?
Presently we only offer guide design against TTTR PAMs suitable for studies involving dCasMINI (Xu et al., 2021).