> 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-gene-expression.md).

# Differential gene expression (DGE) analysis using DESeq2

## We will perform DGE in the following directory

```bash
cd /home/USER/SSAPs
mkdir analysis
mkdir analysis/dge
cd analysis/dge
R
```

## DGE analysis with following quantification inputs

* [Salmon/Kallisto](/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-salmon-input.md)
* [STAR](/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-star-input.md)
* [STAR + RSEM](/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-star-+-rsem-input.md)