GUIDEseq-package {GUIDEseq} | R Documentation |
The package includes functions to retain one read per unique molecular identifier (UMI), filter reads lacking integration oligo sequence, identify peak locations (cleavage sites) and heights, merge peaks, perform off-target search using the input gRNA. This package leverages CRISPRseek and ChIPpeakAnno packages.
Package: | GUIDEseq |
Type: | Package |
Version: | 1.0 |
Date: | 2015-09-04 |
License: | GPL (>= 2) |
Function GUIDEseqAnalysis integrates all steps of GUIDE-seq analysis into one function call
Lihua Julie Zhu Maintainer:julie.zhu@umassmed.edu
Shengdar Q Tsai and J Keith Joung et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotechnology 33, 187 to 197 (2015)
GUIDEseqAnalysis
if(interactive()) { library("BSgenome.Hsapiens.UCSC.hg19") umiFile <- system.file("extdata", "UMI-HEK293_site4_chr13.txt", package = "GUIDEseq") alignFile <- system.file("extdata","bowtie2.HEK293_site4_chr13.sort.bam" , package = "GUIDEseq") gRNA.file <- system.file("extdata","gRNA.fa", package = "GUIDEseq") guideSeqRes <- GUIDEseqAnalysis( alignment.inputfile = alignFile, umi.inputfile = umiFile, gRNA.file = gRNA.file, orderOfftargetsBy = "peak_score", descending = TRUE, keepTopOfftargetsBy = "predicted_cleavage_score", scoring.method = "CFDscore", BSgenomeName = Hsapiens, min.reads = 80, n.cores.max = 1) guideSeqRes$offTargets }