`DESeq2`¶

Let's create a clean fresh history (wheel → Create New) and name it DESeq2
Copy the .Countsdatasets from your STAR/ HISAT2 history to this new history (wheel → Copy datasets)
Select the DESeq2 tool with the following parameters:
1. how: Select group tags corresponding to levels
2. In Factor:
  1. In 1: Factor
    - Specify a factor name: Treatment
    - In Factor level:
      - In 1: Factor level:
        
        Specify a factor level: treated
        
        Counts file(s): the 3 gene count files with treat in their name
      - In 2: Factor level:
        
        Specify a factor level: untreated
        
        Counts file(s): the 4 gene count files with untreat in their name
  2. Click on Insert Factor (not on Insert Factor level)
  3. In 2: Factor
    - Specify a factor name to Sequencing
    - In Factor level:
      - In 1: Factor level:
        
        Specify a factor level: Paired
        
        Counts file(s): the 4 gene count files with paired in their name
      - In 2: Factor level:
        
        Specify a factor level: Single
        
        Counts file(s): the 3 gene count files with single in their name
3. Files have header?: Yes
4. Output normalized counts table: Yes
5. Execute

DESeq2¶