> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-transcript-usage.md).

# Differential transcript usage (DTU) analysis

## We will perform DTU in the following directory

```r
cd /home/USER/SSAPs
mkdir analysis
mkdir analysis/dtu
cd analysis/dtu
R
```

The proposed workflow is adapted from the a 2018 publication authored by [Michael Love, et al. in F1000Res](https://dx.doi.org/10.12688%2Ff1000research.15398.3).

We will use the quantification data generated by Salmon to perform DTU detection by the statistical methods, DRIMSeq and DEXSeq. As proposed in the paper, we will also use stageR to further control the overall false discovery rate (OFDR) across genes and transcripts

1. [DTU analysis using DRIMSeq](/guide-to-rna-seq-analysis/differential-expression-analysis/differential-transcript-usage/dtu-using-drimseq.md)
2. [DTU analysis using DEXSeq](/guide-to-rna-seq-analysis/differential-expression-analysis/differential-transcript-usage/dtu-using-dexseq.md)