## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install(version="devel") # BiocManager::install("crisprBwa") ## ----------------------------------------------------------------------------- library(Rbwa) fasta <- system.file(package="crisprBwa", "example/chr12.fa") outdir <- tempdir() index <- file.path(outdir, "chr12") Rbwa::bwa_build_index(fasta, index_prefix=index) ## ----------------------------------------------------------------------------- library(crisprBwa) library(BSgenome.Hsapiens.UCSC.hg38) data(SpCas9, package="crisprBase") crisprNuclease <- SpCas9 bsgenome <- BSgenome.Hsapiens.UCSC.hg38 spacers <- c("AGCTGTCCGTGGGGGTCCGC", "CCCCTGCTGCTGTGCCAGGC", "ACGAACTGTAAAAGGCTTGG", "ACGAACTGTAACAGGCTTGG", "AAGGCCCTCAGAGTAATTAC") runCrisprBwa(spacers, bsgenome=bsgenome, crisprNuclease=crisprNuclease, n_mismatches=3, canonical=FALSE, bwa_index=index) ## ----eval=TRUE---------------------------------------------------------------- seeds <- c("GTAAGCGGAGTGT", "AACGGGGAGATTG") runBwa(seeds, n_mismatches=2, bwa_index=index) ## ----------------------------------------------------------------------------- sessionInfo()