PGS Documentation

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SubtitleTextConfiguring criteria for transcripts with a p-value < 0.05
AnchorNameConfigure Criterea

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  • In the Configure Criteria dialog box (Figure 2), provide a name for the list (Diff Exp)
  • Select 1/transcripts (RNA-Seq_results.transcripts) from theSpreadsheet drop-down menu 
  • Select 8. p-value(DiffExp) from the Column drop-down menu
  • Set Include p-values to significant with FDR with a value of 0.05

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SubtitleTextConfiguring criteria for a list of alternatively spliced genes
AnchorNameConfiguring Gene List another

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  • Select OK to generate Alt Splice
  • Select both lists in the right-hand panel under the Criteria panel while holding the Ctrl key on your keyboard
  • Select Intersection from the left-hand panel of the List Manager dialog (Figure 4)

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SubtitleTextCreating a gene list at the intersection of two criteria
AnchorNameCreating an Intersection Gene List

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  • Enter a name for the criteria (Diff Exp and Alt Splice
  • Select OK to close the naming dialog and OK again to close the list creation hint dialog
  • Select Save List from the Manage criteria section of the List Manager dialog (Figure 5)

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SubtitleTextSaving a created list criteria
AnchorNameSaving Created List

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  • Select Diff Exp and Alt Splice in the List Creator dialog (Figure 6)

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SubtitleTextSelecting list to save in List Creator dialog
AnchorNameList Creator dialog

 

  • Select OK to save the list
  • Select Close to exit the List Manager dialog and view the Diff_Exp_and_Alt_Splice spreadsheet (Figure 7)

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SubtitleTextA list of the differentially expressed and alternatively spliced genes is now available for downstream analysis
AnchorNameViewing Created List

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This list of differentially expressed and alternatively spliced transcripts will be used later in the next section of the tutorial. 

 

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