## ----cite, eval=TRUE---------------------------------------------------------- citation("Rbowtie") ## ----install, eval=FALSE------------------------------------------------------ # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("Rbowtie") ## ----loadLibraries, eval=TRUE------------------------------------------------- library(Rbowtie) ## ----bowtieBuildUsage, eval=TRUE---------------------------------------------- bowtie_build_usage() ## ----bowtieBuild, eval=TRUE--------------------------------------------------- refFiles <- dir(system.file(package="Rbowtie", "samples", "refs"), full=TRUE) indexDir <- file.path(tempdir(), "refsIndex") tmp <- bowtie_build(references=refFiles, outdir=indexDir, prefix="index", force=TRUE) head(tmp) ## ----bowtieUsage, eval=TRUE--------------------------------------------------- bowtie_usage() ## ----bowtie, eval=TRUE-------------------------------------------------------- readsFiles <- system.file(package="Rbowtie", "samples", "reads", "reads.fastq") samFiles <- file.path(tempdir(), "alignments.sam") bowtie(sequences=readsFiles, index=file.path(indexDir, "index"), outfile=samFiles, sam=TRUE, best=TRUE, force=TRUE) strtrim(readLines(samFiles), 65) ## ----SpliceMap, eval=TRUE----------------------------------------------------- readsFiles <- system.file(package="Rbowtie", "samples", "reads", "reads.fastq") refDir <- system.file(package="Rbowtie", "samples", "refs", "chr1.fa") indexDir <- file.path(tempdir(), "refsIndex") samFiles <- file.path(tempdir(), "splicedAlignments.sam") cfg <- list(genome_dir=refDir, reads_list1=readsFiles, read_format="FASTQ", quality_format="phred-33", outfile=samFiles, temp_path=tempdir(), max_intron=400000, min_intron=20000, max_multi_hit=10, seed_mismatch=1, read_mismatch=2, num_chromosome_together=2, bowtie_base_dir=file.path(indexDir, "index"), num_threads=4, try_hard="yes", selectSingleHit=TRUE) res <- SpliceMap(cfg) res strtrim(readLines(samFiles), 65) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()