## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----install, eval=FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("Rbowtie2") ## ----loading------------------------------------------------------------------ library(Rbowtie2) ## ----idad--------------------------------------------------------------------- td <- tempdir() reads_1 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_1.fq") reads_2 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_2.fq") (adapters <- identify_adapters(file1=reads_1,file2=reads_2, basename=file.path(td,"reads"), "--threads 3",overwrite=TRUE)) ## ----rmad--------------------------------------------------------------------- (cmdout<-remove_adapters(file1=reads_1,file2=reads_2,adapter1 = adapters[1], adapter2 = adapters[2], output1=file.path(td,"reads_1.trimmed.fq"), output2=file.path(td,"reads_2.trimmed.fq"), basename=file.path(td,"reads.base"),overwrite=TRUE,"--threads 3")) ## ----adrmusage---------------------------------------------------------------- adapterremoval_usage() ## ----adrmversion-------------------------------------------------------------- adapterremoval_version() ## ----bt2bd1------------------------------------------------------------------- td <- tempdir() refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"),full=TRUE) (cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), "--threads 4 --quiet", overwrite=TRUE)) ## ----bt2bdusage--------------------------------------------------------------- bowtie2_build_usage() ## ----bt2align----------------------------------------------------------------- reads_1 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads", "reads_1.fastq") reads_2 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads", "reads_2.fastq") if(file.exists(file.path(td, "lambda_virus.1.bt2"))){ (cmdout<-bowtie2(bt2Index = file.path(td, "lambda_virus"), samOutput = file.path(td, "result.sam"), seq1=reads_1,seq2=reads_2,overwrite=TRUE,"--threads 3")) head(readLines(file.path(td, "result.sam"))) } ## ----bt2usage----------------------------------------------------------------- bowtie2_usage() ## ----bt2version--------------------------------------------------------------- bowtie2_version() ## ----sessioninfo-------------------------------------------------------------- sessionInfo()