When attempting to use the compare2sequences tool in CRISPRseek, I received the following error:
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> library(CRISPRseek)
> inputFile1Path <- system.file("extdata", "x",
+ package = "CRISPRseek")
> inputFile2Path <- system.file("extdata", "y",
+ package = "CRISPRseek")
> REpatternFile <- system.file("extdata", "NEBenzymes.fa",
+ package = "CRISPRseek")
> seqs <- compare2Sequences(inputFile1Path, inputFile2Path,
+ outputDir = getwd(),
+ REpatternFile = REpatternFile, overwrite = TRUE)
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory C:/Users/...
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory C:/Users/...
[1] "Scoring ..."
finish off-target search in sequence 2
finish off-target search in sequence 1
finish feature vector building
finish score calculation
Error in .Method(..., deparse.level = deparse.level) :
number of columns of matrices must match (see arg 2)
---------------------------------
Upon contacting Dr. Julie Zhu, she found a bug in compare2sequences that occurs when there are no offtargets for some of the gRNAs. She has updated the master code, though I am unsure if the update is available through Bioconductor yet.