# #设置,包括= FALSE ----------------------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) 选项(宽度= 100)# #——getPackage eval = FALSE ----------------------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,静静地= TRUE) # install.packages (BiocManager) # BiocManager::安装(“Rhisat2 ") ## ---- eval = FALSE -------------------------------------------------------------------------------- # BiocManager::安装(“fmicompbio / Rhisat2 ") ## ------------------------------------------------------------------------------------------------- 库(Rhisat2)## ------------------------------------------------------------------------------------------------- list.files(系统。file("extdata/refs"， package="Rhisat2")， pattern="\\.fa$")文件(“extdata /参”,包=“Rhisat2”),full.names = TRUE,模式= \ \ .fa $) td < - tempdir () hisat2_build(= =参考文献的引用,outdir = td,前缀“myindex”,迫使= TRUE,严格= TRUE,执行= TRUE ) ## ------------------------------------------------------------------------------------------------- 打印(hisat2_build(=参考文献的引用,outdir =道明,前缀= " myindex”,力= TRUE,严格= TRUE,执行= FALSE )) ## ------------------------------------------------------------------------------------------------- list.files(系统。file("extdata/reads"， package="Rhisat2")， pattern="\\.fastq$") read <- list.files(system. extdata .files);文件(“extdata /读取”,包=“Rhisat2”),模式= " \ \。fastq$"， full.names=TRUE)Path (td， "myindex")， type="paired"， outfile=file。路径(td,“out.sam”),迫使= TRUE,严格= TRUE,执行= TRUE ) ## ------------------------------------------------------------------------------------------------- spsfile < - tempfile () gtf < -执行(“extdata /文献/基因。(features=gtf, outfile=spsfile)Path (td， "myindex")， type="paired"， outfile=file。path(td， "out_sps.sam")， ' known-splicesite-infile ' =spsfile, force=TRUE, strict=TRUE，执行= TRUE ) ## ------------------------------------------------------------------------------------------------- hisat2_version () ## ------------------------------------------------------------------------------------------------- hisat2_build_usage () # #------------------------------------------------------------------------------------------------- hisat2_usage () ## ------------------------------------------------------------------------------------------------- sessionInfo ()