# 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](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-salmon-input)
* [STAR](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-star-input)
* [STAR + RSEM](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-star-+-rsem-input)


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