# # # R代码从装饰图案的Rsubread来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:Rsubread。Rnw: 70 - 73 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(Rsubread) ref < - - - - - -执行(“extdata”、“reference.fa”,包=“Rsubread”) buildindex (basename =“reference_index”,引用= ref) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:Rsubread。Rnw: 90 - 92 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #读< -执行(“extdata”、“reads.txt.gz”,包=“Rsubread”)一致。统计< -对齐(指数=“reference_index readfile1 =读取,output_file =“alignResults.BAM phredOffset = 64) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:Rsubread。Rnw: 99 - 103 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # reads1 < -执行(“extdata”、“reads1.txt.gz”,包=“Rsubread”) reads2 < -执行(“extdata”、“reads2.txt.gz”,包=“Rsubread”)一致。stat2 < -对齐(指数=“reference_index readfile1 = reads1 readfile2 = reads2 output_file =“alignResultsPE.BAM phredOffset = 64) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:Rsubread。Rnw: 125 - 135 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #安< - data.frame (GeneID = c (“gene1”、“gene1”、“gene2”、“gene2”),装备=“chr_dummy”,开始= c(100, 1000, 3000, 5000),结束= c(500, 1800, 4000, 5500),链= c (“+”、“+”、“-”,“-”), stringsAsFactors = FALSE)安fc_SE <——featureCounts (“alignResults.BAM”, annot.ext =安)fc_SE # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:Rsubread。Rnw: 142 - 144 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # fc_PE <——featureCounts (“alignResultsPE.BAM annot.ext =安,isPairedEnd = TRUE) fc_PE # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:Rsubread。Rnw: 164 - 166 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # x <——qualityScores(文件名=读取,抵消= 64,nreads = 1000) x(1:10, 1:10) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:Rsubread。Rnw: 191 - 192 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # propmapped (“alignResults.BAM”)