Question

Error Searching for gRNAs ...

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krababah • 0

@krababah-10712

Last seen 8.5 years ago

Hi,

I kindly need help finding a solution for the problem. While trying to execute the command:

offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE,

REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens,txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 3, chromToSearch = "",outputDir = outputDir, overwrite = TRUE)

I have executed the the following two commands (before the above): inputFilePath <- " C:\\Users\\S\\Documents\\x.fa" and

REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek") // here i dont know what is "extdata" and also i dont know the file "NEBenzymes.fa" is located

I got the error :

Validating input ...
Searching for gRNAs ...
Error in findgRNAs(inputFilePath, findPairedgRNAOnly = findPairedgRNAOnly,  : 
  inputfile specified as  C:\Users\S\Documents\x.fa does not exists!
In addition: Warning message:
In dir.create(outputDir) : 'C:\Users\S\Documents' already exists

I have the x.fa in the specified location as text file and its contents is

>rs362331C
GACCCACGCCTGCTCCCTCATCCACTGTGTGCACTTCATCCTGGA

Thanks

crisprseek • 914 views

ADD COMMENT • link updated 8.5 years ago by Julie Zhu ★ 4.3k • written 8.5 years ago by krababah • 0

score 0 · Answer 1 · 2016-05-17

Khaleel, The error message indicates that x.fa cannot be found. Could you please try to read it into R using readDNAStringSet function? readDNAStringSet(inputFilePath). If it is not successful, that means the file path is not correct. Could you please try to set inputFilePath <- "C:/Users/S/Documents/x.fa" and see if it works? Could you please also try the sample code and see if it works and print the session info? sessionInfo() library(CRISPRseek) library("BSgenome.Hsapiens.UCSC.hg19") library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) outputDir <- getwd() inputFilePath <- system.file("extdata", "inputseq.fa", package = "CRISPRseek") REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek") results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, annotatePaired = FALSE, BSgenomeName = Hsapiens, chromToSearch = "chrX", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, outputDir = outputDir, overwrite = TRUE) NEBenzymes.fa is included in the package. Since you are setting findgRNAsWithREcutOnly = FALSE, you do not have to set REpatternFIle. I noticed that you chromToSearch = "", which means that you areinterested in finding gRNAs without searching for offTargets. Please take a look at the examples at http://bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf. Best regards, Julie From: "krababah [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+f9627716+code@bioconductor.org<mailto:reply+f9627716+code@bioconductor.org>" <reply+f9627716+code@bioconductor.org<mailto:reply+f9627716+code@bioconductor.org>> Date: Tuesday, May 17, 2016 2:44 AM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] Error Searching for gRNAs ... Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User krababah<https: support.bioconductor.org="" u="" 10712=""/> wrote Question: Error Searching for gRNAs ...<https: support.bioconductor.org="" p="" 82705=""/>: Hi, I kindly need help finding a solution for the problem. While trying to execute the command: offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens,txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 3, chromToSearch = "",outputDir = outputDir, overwrite = TRUE) I have executed the the following two commands (before the above): inputFilePath <- "C:\\Users\\S\\Documents\\x.fa" and REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek") // here i dont know what is "extdata" and also i dont know the file "NEBenzymes.fa" is located I got the error : Validating input ... Searching for gRNAs ... Error in findgRNAs(inputFilePath, findPairedgRNAOnly = findPairedgRNAOnly, : inputfile specified as C:\Users\S\Documents\x.fa does not exists! In addition: Warning message: In dir.create(outputDir) : 'C:\Users\S\Documents' already exists I have the x.fa in the specified location as text file and its contents is >rs362331C GACCCACGCCTGCTCCCTCATCCACTGTGTGCACTTCATCCTGGA Thanks ________________________________ Post tags: crisprseek You may reply via email or visit Error Searching for gRNAs ...