What tools do you use to find the potential off-target sites when designing Cas9/Cas12 RNA-guided endonucleases?
What are the alternatives beyond Cas-offinder to find potential off-target sites when designing sgRNAs? My primary concern with Cas-offinder is that it overlooks indels/gaps.
Are there computational tools to list all the off-sites? Are there tools that use existing aligners such as BWA or Bowtie2 and find potential off-target sites?
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CCTop uses bowtie2 to align sgRNA candidates to a provided genome. For the standalone version you could use a custom genome, but that obviously requires that you have a custom high-quality genome assembly. Do you have that, and does the reference genome not suffice?
I will use hg19 or hg38 for human, mm10 for mouse and one assembly I have improved for a fly after polishing dmel6.
It depends on how fancy you want the results to be. I just use old blastn with appropriate parameters.