DESeq2


  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