Discrepancy between easy_prime web output and cli output

[marcus-r-kelly]

Thank you for this excellent tool!

I am wondering about a discrepancy I find between the webtool and a local install.
Specifically, submitting the following variant:

• Chromosome : chr12
• Position : 25398281
• Reference : CCACCA
• Alternative : CCAACG

Produces different efficiency estimates with the tool as installed by conda following the directions.
Specifically, the best solution in both cases is this :

But the installed efficiency estimate is 0.47. Is the command-line tool given out of 1.0 instead of 100%? Are there other reasons these should be so different?

[YichaoOU]

Thanks!

Yes, the predicted_efficiency in topX_pegRNAs.csv is from 0 to 1. If you multiply it by 100, you have the percentage.

I'm not sure why, even though they gave the same pegRNA, the predicted efficiency is different. When I used the local version, I also got 0.47004926204681396.

One thing I want to mention is that, for the vcf format, I would assume there is no overlap between ref and alt. Right now, your ref is CCACCA and your alt is CCAACG, I think it should CCA and ACG. The beginning CCA should be removed because these positions are unchanged. And then the Position becomes 25398281+3.

[marcus-r-kelly]

One thing I want to mention is that, for the vcf format, I would assume there is no overlap between ref and alt. Right now, your ref is CCACCA and your alt is CCAACG, I think it should CCA and ACG. The beginning CCA should be removed because these positions are unchanged. And then the Position becomes 25398281+3.

I have sanitized my variants and this fixed an entirely unrelated issue where command-line easyprime would produce pegRNAs encoding indels not described in the input variants. However, it did not change the discrepancy between the webtool and the command line utility.