https://mp.weixin.qq.com/s/FCQylK0RjAZgFEzikB1DyQ

生信技能树  2019-11-07

一图看懂DGE, DTE and DTU

参考文献：F1000Research 2019, 8:213 Last updated: 18 MAR 2019


今天学习rnaseqDTU

我们首先看看转录组领域的基因表达相关流程吧，首先一起学习的是Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

http://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html
这个就没有中文版了，实际上是使用salmon软件把我们的RNA-seq测序的fastq数据根据参考转录组进行定量后，走几个R包流程。

在R里面安装这个bioconductor流程

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rnaseqDTU")
因为原文写的实在是太详细了，我这里就不拷贝粘贴了，大家直接去阅读即可：

RNA-seq workflow for differential transcript usage following Salmon
quantification
http://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.R
全部目录如下；

3 Methods
3.1 Simulation
3.2 Operation
3.3 Quantification and data import
3.4 DTU testing
4 Workflow
4.1 Salmon quantification
4.2 Importing counts into R/Bioconductor
4.3 Transcript-to-gene mapping
5 Statistical analysis of differential transcript usage
5.1 DRIMSeq
5.2 stageR following DRIMSeq
5.3 Post-hoc filtering on the standard deviation in proportions
5.4 DEXSeq
5.5 stageR following DEXSeq
5.6 Citing methods in published research
6 DTU analysis complements DGE analysis
6.1 DGE analysis with DESeq2
6.2 DGE analysis with edgeR
6.3 End of workflow section
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