Question

CRISPRseek package: findgRNAs error

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nderian ▴ 10

@95b5814b

Last seen 2.8 years ago

Denmark

Hi,

While looking for gRNAs in a test sequence, I faced the following message:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'args' in selecting a method for function 'do.call': key 73 (char 'e') not in lookup table

Here the setting I used:

data<-"AAGAGGACACGCGCGCTCACACCCGCCCCTGGGAGCAGAAGCAGTATCTTCCCCAGCTTCGTGGGTTTCTCCTCCCCCCGGAGTCAGGGTGTGCGAG"
input<-DNAStringSet(data)
names(input)<-"test"

findgRNAs(input,PAM = "YTTN",
          PAM.size=4,
          gRNA.size = 38,
          PAM.location = "5prime",
          annotatePaired=FALSE)

I understood the (char 'e') is coming for the sequence name. Actually, it tries to put the sequence name into a DNAstringSet. But I do not understand why it does it. The same analysis with the following sequence is working perfectly:

data<-"ACTTCCTCCGGCTTCTTCACCTCTAGGAAATCTCGGGGCTTCGCTCTATCGAGAGTGCTCGTCAAGGGTGATTCTTGATCACCACCATCCAGTAGTGCTGGCGTCCGAATGCATATCCTTTTGCCTTGCAAAGAAGAGTCATGAACTTCAAAACCCCCGAGACGGATCATTAATCCTGCTTTGCAGGAAAGGAAAACCCTCCATTCCCAGCCACCGGCCACCCCTCTCCGCAGACTGCAACCGCGGAGGCGCTCGGAGCCG" 
input<-DNAStringSet(data)
names(input)<-"test"

findgRNAs(input,PAM = "YTTN",
          PAM.size=4,
          gRNA.size = 38,
          PAM.location = "5prime",
          annotatePaired=FALSE)

So it has to do with the sequence itself, could it be too short to be fully exploitable?

Thank you in advance for your feedback.

sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

CRISPRseek • 1.0k views

ADD COMMENT • link 3.1 years ago nderian ▴ 10

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Hi nderian,

There was a bug in findgRNAs::.getgRNA.cut.sites(). I have fixed it, detailed see this pull request.

For a quick fix, you can download and source the findgRNAs.R from this repo inside your R session: https://github.com/hukai916/CRISPRseek

library(CRISPRseek)

download.file("https://raw.githubusercontent.com/hukai916/CRISPRseek/master/R/findgRNAs.R", destfile = "findgRNAs.R")
source("findgRNAs.R")

data<-"AAGAGGACACGCGCGCTCACACCCGCCCCTGGGAGCAGAAGCAGTATCTTCCCCAGCTTCGTGGGTTTCTCCTCCCCCCGGAGTCAGGGTGTGCGAG"
input<-DNAStringSet(data)
names(input)<-"test"

findgRNAs(input,PAM = "YTTN",
          PAM.size=4,
          gRNA.size = 38,
          PAM.location = "5prime",
          annotatePaired=FALSE)

Output:

DNAStringSet object of length 1:
    width seq                                               names
[1]    42 CTTCCCCAGCTTCGTGGGTTTCTCCTCCCCCCGGAGTCAGGG        test_gR68f

ADD REPLY • link 3.1 years ago Kai Hu ▴ 70

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Thank you very much for the update and bug fix Kai.

Best.

ADD REPLY • link 3.1 years ago nderian ▴ 10