比如转录组,之前是HTSeq流程的数据,现在是STAR-Counts的数据。具体的数据信息参考: https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320 下载后的数据,打开是这样的。都放在了一个文件中。 这里分享一下怎么提取数据。 数据的下载和之前的教程一样【14-TCGA数据库下载整理】。
Counts数据 提供了Non-stranded Counts和Stranded Counts数据 。 Non-stranded RNA-Seq与Stranded RNA-seq的建库方法有所不同,有文献(DOI: 10.1186/s12864-015-1876-7)分析认为Stranded RNA-seq 得到的mRNA数据更为准确。 但是,对于大多数的分析来说,Non-stranded RNA-Seq数据用于常规分析已经足够(https://web.aze...
2.在跳转的页面中,点击RNA-Seq后面的数字 3. 在新打开的页面中,点击左上角的Files 4.接下来就是不一样的地方了,可以看到在workflow type里面没有HTSeq-Counts了,取而代之的是STAR-Counts。我们就选择这个STAR-Counts。 你会发现STAR-Counts里面有88个文件,其中44个是Gene Expression Quantification,这是我们合并...
Next we need to generate custom bed files for every individual. These files must contain only exonic SNPs that are heterozygous in that individual. This is necessary because CountSNPASE will randomly choose a SNP to count if more than one SNP is present in a read. As some RNA-seq reads ...
"fpkm_uq_unstranded" 对于文件中的信息 下面就可以获取数据了,想要什么就获取什么。一般就是TPM和FPKM。 jsonFileInfo<-processingJsonFiles(jsonFile="metadata.cart.2022-04-05.json")filepath=dir(path="./data",pattern="counts.tsv$",full.names=T,recursive=T)dat=getTCGA_RNAseq_data(filepath=filepa...
Non-stranded RNA-Seq, on the other hand, is often sufficient for measuring gene expression in organisms with well-annotated genomes. 2. 更新后的TCGA RNA-seq数据的下载与读取 数据更新后,一些既往常用的数据下载和读取方法有所变化,本着“喂(bu)饭(yan)到(qi)口(fan)”的分享精神,此次我们重点介绍2...
"fpkm_uq_unstranded" 对于文件中的信息 下面就可以获取数据了,想要什么就获取什么。一般就是TPM和FPKM。 jsonFileInfo<-processingJsonFiles(jsonFile="metadata.cart.2022-04-05.json")filepath=dir(path="./data",pattern="counts.tsv$",full.names=T,recursive=T)dat=getTCGA_RNAseq_data(filepath=filepa...
Non-stranded RNA-Seq, on the other hand, is often sufficient for measuring gene expression in organisms with well-annotated genomes. 2. 更新后的TCGA RNA-seq数据的下载与读取 数据更新后,一些既往常用的数据下载和读取方法有所变化,本着“喂(bu)饭(yan)到(qi)口(fan)”的分享精神,此次我们重点介绍2...
Non-stranded RNA-Seq, on the other hand, is often sufficient for measuring gene expression in organisms with well-annotated genomes. 2. 更新后的TCGA RNA-seq数据的下载与读取 数据更新后,一些既往常用的数据下载和读取方法有所变化,本着“喂(bu)饭(yan)到(qi)口(fan)”的分享精神,此次我们重点介绍2...
Non-stranded RNA-Seq, on the other hand, is often sufficient for measuring gene expression in organisms with well-annotated genomes. 2. 更新后的TCGA RNA-seq数据的下载与读取 数据更新后,一些既往常用的数据下载和读取方法有所变化,本着“喂(bu)饭(yan)到(qi)口(fan)”的分享精神,此次我们重点介绍2...