Entering edit mode
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>
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