DESeq2

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1. Let's create a clean fresh history (wheel --> Create New) and name it DESeq2
2. Copy the .Countsdatasets from your STAR/ HISAT2 history to this new history (wheel --> Copy datasets)
3. 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