maximilianh
commented
1 month ago offtargetCount - how do you calculate that? what is the reference of the off targets? how many mismatches you allowed in the command line?
Calculation: just counting. reference is the genome. mismatches are up to 5 (I think, there is a command line option for this) and it's not allowing all non-canonical PAMs, see the manual page, there is a complicated rule on non-canonical PAM matches in off-targets, justified in the paper.
GrafEtAlStatus - what is the meaning of this column, and what are the abbreviations that is used in it?
This was a somewhat strange paper, but a few users wanted this. It's the graf et al paper, see the manual or the graphical output, mouse over the info icon of this column.
Does the order of the rows in the output table has a meaning, such as rating the gRNAs?
They should be sorted by specificity score? But if not, then just sorted them again, this should be easy on the command line with sort -k
Thanks in advance, and thank you again for the previous helpful replies, Nofar :-]
No problem!
Message ID: @.***>
Hello :)
The code ran successfully (thank you for that), and now I'm trying to understand each column in the output table. The ones that are mentioned in the paper are clear (such as off-target scores and the efficiencies scores), but there are several columns that I want to ask about (and I struggled to find the answers in the code itself (I'm kind of new in this :)) -
offtargetCount - how do you calculate that? what is the reference of the off targets? how many mismatches you allowed in the command line?
GrafEtAlStatus - what is the meaning of this column, and what are the abbreviations that is used in it?
Does the order of the rows in the output table has a meaning, such as rating the gRNAs?
Thanks in advance, and thank you again for the previous helpful replies, Nofar :-]