Closed liu-zhiyang closed 7 months ago
Hi @liu-zhiyang,
Could you provide the two GRanges object files here (upstream
and downstream
) to help me debug?
Hi @liu-zhiyang,
Could you provide the two GRanges object files here (
upstream
anddownstream
) to help me debug?
Apologize for delayed response! Here are the two GRanges, thanks for your reply! downstream.csv upstream.csv
Hi @liu-zhiyang, thanks for the files, that was helpful.
The problem comes from the fact that the function was designed to find all paired guides between all combinations of genomic coordinates between x1 and x2; to find all paired guides in a row-wise manner between x1 and x2, you can use the following code:
ks <- seq_along(upstream)
pairs <- lapply(ks, function(k){
findSpacerPairs(x1=upstream[k],
x2=downstream[k],
bsgenome=bsgenome,
crisprNuclease=SpCas9)
})
pairs <- do.call("c", pairs)
Hi, I am trying to use crisprVerse for paired gRNA design. But when I ran the
findSpacerPairs
function, it returned an error.And here is my input.
Do you have any suggestion about this error? Thank you very much!