Analysis of GUIDE-seq

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Description

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.

Details

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

Author(s)

Lihua Julie Zhu Maintainer:julie.zhu@umassmed.edu

References

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)

See Also

GUIDEseqAnalysis

Examples

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    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
   }