一般就是TPM和FPKM。 jsonFileInfo<-processingJsonFiles(jsonFile="metadata.cart.2022-04-05.json")filepath=dir(path="./data",pattern="counts.tsv$",full.names=T,recursive=T)dat=getTCGA_RNAseq_data(filepath=filepath,jsonFileInfo=jsonFileInfo,data_type="fpkm_unstranded")head(dat)[,1:5] 原...
一般就是TPM和FPKM。 代码语言:javascript 复制 jsonFileInfo <- processingJsonFiles(jsonFile = "metadata.cart.2022-04-05.json ") filepath = dir(path = "./data", pattern = "counts.tsv$", full.names = T, recursive = T) dat = getTCGA_RNAseq_data(filepath =filepath, jsonFileInfo = ...
使用RSEM定量时,需要先构建索引文件,而featureCounts 和HTSeq-count用比对结果直接定量,显得方便很多,而且对于不会写提取counts脚本的用户来说,RSEM构建表达矩阵的命令同样让人惊喜。RSEM定量后的结果更加多样,有gene_id和transcript_id两类。而且count、TPM、FPKM都有,为后续差异分析提供便利。但featureCounts 和HTSeq-co...
$ srun --mem=128G --cpus-per-task=20 --time=2:00:00 --pty STAR \ --runThreadN 40 \ #线程数 --runMode alignReads \#比对模式 --readFilesCommand zcat \#说明你的fastq文件是压缩形式的,就是.gz结尾的,不加的话会报错 --quantMode TranscriptomeSAM GeneCounts \ #将reads比对至转录本序列 ...
STAR比对参数很多,其中有一个quantMode,可以指定--quantMode GeneCounts输出STAR计算出的reads计数结果。(更多常用参数见STAR比对线程也不是越多越好,多少是好?) 格式如下,有4列,各自解释如下: trt_N061011.ReadsPerGene.out.tab: 每个基因的reads count,链非特异性RNASeq选第2列。 column 1: gene ID column...
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#abundance.tsv 列:gene counts TPM kallisto建立索引kallisto定量结果 5.差异基因分析: R install install.packages("ggrepel")install.packages("ggplot2") ### 差异表达 mkdir 06deseq_out #构建表达矩阵 rsem-generate-data-matrix *rsem.genes.results > output.matrix...
(res), as.data.frame(counts(dds, normalized=TRUE)),by="row.names",sort=FALSE)resdata<-merge(as.data.frame(res),as.data.frame(counts(dds,normalized=TRUE)),by="row.names",sort=FALSE)#将fpkm加入分析结果中#resdata <- merge(as.data.frame(res), as.data.frame(read.table(paste0(file_...
filepath=dir(path="./data",pattern="counts.tsv$",full.names=T,recursive=T) jsonFileInfo是processingJsonFiles函数获取的结果。 data_type是下面中的一种。 "unstranded"; "stranded_first"; "stranded_second"; "tpm_unstranded"; "fpkm_unstranded"; ...
{i} \ --outSAMstrandField intronMotif \ --outFilterIntronMotifs None \ --alignSoftClipAtReferenceEnds Yes \ --quantMode TranscriptomeSAM GeneCounts \ --outSAMtype BAM SortedByCoordinate \ --outSAMunmapped Within \ --genomeLoad NoSharedMemory \ --chimSegmentMin 15 \ --chimJunctionOverhang...