Open marcus-r-kelly opened 1 year ago
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.
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.
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:
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?