Hi Miri,

if your sequence is aligned and therefore you have a bam file, you can with command line filter the off-targets (reads) defined by your CRISPR supplier. But even in this case you'll have off targets results since those prediction tools can't take in charge variants and structures you'll have in your sample.

instead of this why not analyzing your RNAseq with the whole data and have a look at the off-targets sites to see if they were targeted?

fred

Hi Miri,

check out Cas-OFFinder. Depends on what organism you work with if the genome is available or not there.