CRISPRme output about crisprme HOT 1 CLOSED

Hi Meltem,

Thanks for trying out CRISPRme and for your question! Sorry for the delayed reply on our end.

I believe this is a feature, not a bug. As you point out, the actual OT sequence reported is identical in both scenarios, but they are alternative alignments relative to each other. The main output of CRISPRme is our "integrated_results" file, which I would encourage you to take a look at if possible. It reports a single candidate off-target site per genomic region by highest CFD score (cutting frequency determination score, an empirically derived metric of predicted cleavage potential from Doench et al. Nat Biotechnol 2016) as well as fewest mismatches + bulges, merging all possible off-target sequences and alternative alignments thereof (as in your example) within a 3 bp window by default. I would suggest that you refer to that as the main CRISPRme results file.

Please let us know if you have any further questions!

Thanks,
Linda

from crisprme.