Question: CRSIPRseek: no summary file generated
0
gravatar for Julie Zhu
5.4 years ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:
Mike, Finally I figured out the problem. It is not a bug. It is the searching criteria max.mismatch =5 and filtering criteria min.score = 0.5. If you set max.mismatch = 5 and min.score = 0.1. The summary file will be there. What happened is that with your initial parameter setting, there is no off-target found. Maybe I should have the function to print out “No off target found with your searching and filtering criteria”. Best regards, Julie On 8/4/14 11:03 AM, "Brodsky, Michael" <michael.brodsky@umassmed.edu> wrote: Hi. I tried two more tests. First, I ran the same script on Rstudio on the cluster. The cluster packages are all the standard (not development) version of R and do not give the Warning message for R version 3.1.1. So, it is NOT due to using a different version of R for the packages. Second, there is only one target site in the fasta file, so I also ran it with find gRNA = TRUE. This gave the same problem where the summary file does not list any gRNAs. Mike On Aug 4, 2014, at 10:50 AM, Michael Brodsky wrote: Hi Julie, Here is the first problem. I ran an off target analysis with existing target site (find gRNA = FALSE). I got a good off target file, but the summary file is blank. I have attached the input file and the command set. The session info is below. I got a warning that I used a more recent (developer?) version of R to construct the packages. Do I need to uninstall and reinstall these? thanks, mike Warning messages: 1: package ‘CRISPRseek’ was built under R version 3.1.1 2: package ‘Biostrings’ was built under R version 3.1.1 3: package ‘IRanges’ was built under R version 3.1.1 4: package ‘GenomeInfoDb’ was built under R version 3.1.1 5: package ‘GenomicRanges’ was built under R version 3.1.1 Warning messages: 1: package ‘GenomicFeatures’ was built under R version 3.1.1 2: package ‘AnnotationDbi’ was built under R version 3.1.1 R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.63 (6734) x86_64-apple-darwin10.8.0] [Workspace restored from /Users/brodsky/.RData] [History restored from /Users/brodsky/.Rapp.history] > getwd() [1] "/Users/brodsky/Desktop/current/Nuclease_projects/inProgress/Freem an_tobi1/tobi2_test" > library(CRISPRseek) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biostrings Loading required package: S4Vectors Loading required package: IRanges Loading required package: XVector Loading required package: BSgenome Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: rtracklayer Warning messages: 1: package ‘CRISPRseek’ was built under R version 3.1.1 2: package ‘Biostrings’ was built under R version 3.1.1 3: package ‘IRanges’ was built under R version 3.1.1 4: package ‘GenomeInfoDb’ was built under R version 3.1.1 5: package ‘GenomicRanges’ was built under R version 3.1.1 > library("BSgenome.Dmelanogaster.UCSC.dm3") > library("TxDb.Dmelanogaster.UCSC.dm3.ensGene") Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:BSgenome’: species The following object is masked from ‘package:GenomeInfoDb’: species Warning messages: 1: package ‘GenomicFeatures’ was built under R version 3.1.1 2: package ‘AnnotationDbi’ was built under R version 3.1.1 > outputDir <- getwd() > inputFilePath <- "tobi2.fa" > REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek") > > offTargetAnalysis(inputFilePath, findgRNAs = FALSE, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Dmelanogaster, txdb = TxDb.Dmelanogaster.UCSC.dm3.ensGene, max.mismatch = 3, chromToSearch = "all", outputDir = outputDir, overwrite = TRUE) Validating input ... >>> Finding all hits in sequences chr2L ... >>> DONE searching >>> Finding all hits in sequences chr2R ... >>> DONE searching >>> Finding all hits in sequences chr3L ... >>> DONE searching >>> Finding all hits in sequences chr3R ... >>> DONE searching >>> Finding all hits in sequences chr4 ... >>> DONE searching >>> Finding all hits in sequences chrX ... >>> DONE searching >>> Finding all hits in sequences chrU ... >>> DONE searching >>> Finding all hits in sequences chrM ... >>> DONE searching >>> Finding all hits in sequences chr2LHet ... >>> DONE searching >>> Finding all hits in sequences chr2RHet ... >>> DONE searching >>> Finding all hits in sequences chr3LHet ... >>> DONE searching >>> Finding all hits in sequences chr3RHet ... >>> DONE searching >>> Finding all hits in sequences chrXHet ... >>> DONE searching >>> Finding all hits in sequences chrYHet ... >>> DONE searching >>> Finding all hits in sequences chrUextra ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done. Please check output files in directory /Users/brodsky/Desktop/c urrent/Nuclease_projects/inProgress/Freeman_tobi1/tobi2_test/ > <tobi2_rscript.txt><tobi2.fa> [[alternative HTML version deleted]]
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ADD COMMENTlink modified 4.7 years ago by Dawid G. Nowak10 • written 5.4 years ago by Julie Zhu4.1k
Answer: CRSIPRseek: no summary file generated
0
gravatar for Dawid G. Nowak
4.7 years ago by
United States
Dawid G. Nowak10 wrote:

Hi Julie,

I have also noticed that in my analysis Summary.xls file was not created. I was trying to use different searching criteria: max.mismatch=5 and filtering criteria min.score = 0.1 etc. I used previously my code for other genes without problems. I am getting also this error and 50 warnings (not attached). 

 

Error in this.score$symbol[query.ind] = overlapGenes.symbol : NAs are not allowed in subscripted assignments

In addition: There were 50 or more warnings (use warnings() to see the first 50)

Any thoughts?

Thanks,

Dawid

 

My setting below:


offTargetAnalysis(inputFilePath,

                    REpatternFile = REpatternFile,

                    format = "fasta",

                    findgRNAsWithREcutOnly = FALSE,

                    findPairedgRNAOnly = FALSE,

                    gRNA.name.prefix = "g.",                 

                    orgAnn = org.Hs.egSYMBOL,

                    BSgenomeName = Hsapiens,

                    txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,

                    chromToSearch="all",

                    min.gap = 0, max.gap = 20,

                    max.mismatch = 5,

                    min.score = 0.1, 

                    topN = 100,

                    topN.OfftargetTotalScore= 10, 

                    annotateExon = TRUE,

                    fetchSequence = TRUE, upstream = 250, downstream = 250,

                    overlap.gRNA.positions = c(17, 18), 

                    outputDir = outputDir,

                    overwrite = TRUE)

 

ADD COMMENTlink written 4.7 years ago by Dawid G. Nowak10
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