Sir, It is not working according to your guidance.
My location of exdata folder is "C:\Users\SUSHOVAN\Documents\R\win-library\3.4\CRISPRseek\extdata" , where I have put two similar fasta sequences X1.fa and X2.fa I have tried to run the following code and got that error. The file fize of X1.fa and X2.fa is 1 Kb and 1Kb. variation among the sequences is about 10%-20%.
I cut and paste from X1 and X2.fa to the predefined , preexisting files rs362331C.fa and rs362331T.fa
but same problem.
What is the meaning of 'x' has "out of limits" views
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
<simpleError in fromXStringViewsToStringSet(x, out.of.limits = out.of.limits, use.names = use.names): 'x' has "out of limits" views>
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
<simpleError in fromXStringViewsToStringSet(x, out.of.limits = out.of.limits, use.names = use.names): 'x' has "out of limits" views>
[1] "Scoring ..."
Error in searchHits(gRNAs = gRNAs1, PAM = PAM, PAM.pattern = PAM.pattern, :
object 'gRNAs1' not found
In addition: Warning messages:
1: In dir.create(outputDir) :
'C:\Users\SUSHOVAN\Documents\rs362331C.fa-Aug-19-2017' already exists
2: In dir.create(outputDir) :
'C:\Users\SUSHOVAN\Documents\rs362331T.fa-Aug-19-2017' already exists
> inputFile1Path <- system.file("extdata", "rs362331C.fa", package = "CRISPRseek")
> inputFile1Path <- system.file("extdata", "rs362331C.fa", package = "CRISPRseek")
> inputFile2Path <- system.file("extdata", "rs362331T.fa", package = "CRISPRseek")
> seqs <- compare2Sequences(inputFile1Path, inputFile2Path,outputDir = outputDir , REpatternFile = REpatternFile,overwrite = TRUE)
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
<simpleError in fromXStringViewsToStringSet(x, out.of.limits = out.of.limits, use.names = use.names): 'x' has "out of limits" views>
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
<simpleError in fromXStringViewsToStringSet(x, out.of.limits = out.of.limits, use.names = use.names): 'x' has "out of limits" views>
[1] "Scoring ..."
Error in searchHits(gRNAs = gRNAs1, PAM = PAM, PAM.pattern = PAM.pattern, :
object 'gRNAs1' not found
In addition: Warning messages:
1: In dir.create(outputDir) :
'C:\Users\SUSHOVAN\Documents\rs362331C.fa-Aug-19-2017' already exists
2: In dir.create(outputDir) :
**************** Should I give very small sequence for comparing two sequence with only 1SNP.
***************** My input files were about 1Kb with 10-20 % variation (of nucleotide between those files).
Sir/Madam please help me
Thank u Julie, but
My question was about the length of the sequences and the difference between them.
Please see the the question
**************** Should I give very small sequence for comparing two sequence with only 1SNP.
***************** My input files were about 1Kb with 10-20 % variation (of nucleotide between those files).