## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install(version="devel") # BiocManager::install("crisprBowtie") ## ----------------------------------------------------------------------------- library(Rbowtie) fasta <- file.path(find.package("crisprBowtie"), "example/chr1.fa") tempDir <- tempdir() Rbowtie::bowtie_build(fasta, outdir=tempDir, force=TRUE, prefix="myIndex") ## ----warning=FALSE, message=FALSE--------------------------------------------- library(crisprBowtie) data(SpCas9, package="crisprBase") crisprNuclease <- SpCas9 spacers <- c("TCCGCGGGCGACAATGGCAT", "TGATCCCGCGCTCCCCGATG", "CCGGGAGCCGGGGCTGGACG", "CCACCCTCAGGTGTGCGGCC", "CGGAGGGCTGCAGAAAGCCT", "GGTGATGGCGCGGGCCGGGC") runCrisprBowtie(spacers, crisprNuclease=crisprNuclease, n_mismatches=3, canonical=FALSE, bowtie_index=file.path(tempDir, "myIndex")) ## ----eval=TRUE---------------------------------------------------------------- seeds <- c("GTAAAGGT", "AAGGATTG") runBowtie(seeds, n_mismatches=2, bowtie_index=file.path(tempDir, "myIndex")) ## ----------------------------------------------------------------------------- sessionInfo()