If you are following a Combine and/or Reanalyze Assemblies workflow on a local machine, the Input Assemblies and Define Individual Replicates screen is where you add, name and group the assemblies, and select a type for each assembly (e.g., RNA-Seq, CNV, etc.). The bottom of the screen lets you view the ChIP-seq assemblies (if any) and their controls.

The screen is similar to the Input Sequence Files and Define Experiments or Individual Replicates screen.

To add or remove assemblies:

All assemblies must have been created using the same reference sequence. Add assemblies using the Add button. Add all assemblies within a folder using the Add or Add Folder button. In the file explorer, navigate to and select the desired assembly or folder and then click Open.

If you would like to remove an assembly from the list, select it and click Remove.

To group replicate sets:

  • To name replicates manually and place them in groups, select one or more rows using click, Ctrl+click, Cmd+click or Shift+click and then press the Group Selected button to group the experiments and give them a single shared name. Type the name into the Enter Replicate Set Name for Selected Reads dialog and click OK. All selected rows will now share the same “Individual Replicate” name, and read files will be separated into individual sample files based on these custom names.

  • To enter a single replicate name manually, click on a single “Individual Replicate” cell and type in a name.

  • To remove replicate names, select one or more rows using click, Ctrl+click, Cmd+click or Shift+click and then press the Ungroup Selected button. In the selected rows, the “Experiment” column will return to its original (blank) state.

To specify the workflow type:

The Workflow must be specified for each assembly in this screen using the drop-down menus in each row. Choices are RNA-Seq, ChIP-Seq, CNV-Seq, miRNA or Other (default). You cannot proceed to the next screen until a non-Other option has been selected for each row.

Once you are finished making choices in this screen, click Next > to continue to the next wizard screen.

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