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Torrent Suite Software space on Ion Community

User Interface Guide TOC

Work with Completed Runs

To begin a sequencing run, see Templates , Planned Runs , and Plan by Sample Set .

Reanalyze a run

To reanalyze a run, see Reanalyze a Completed Run . When you reanalyze a run, you have to option to change the run's settings.

Add a run to a project

In the Data tab Completed Runs & Reports page table view, you can add a completed run to a project. (You optionally create projects to group your runs. For more information, see Projects Tab .)

The following list describes advantages of grouping your results sets into projects:

• Combine multiple result sets into one (useful to later analyze as a single run)

• Export result sets to another system for additional analysis

• Group result sets into projects for convenient tracking and bulk data management

Follow these steps to add a completed run to a project:

1. Go to the Data > Completed Runs & Reports page and click List View .
   
   
   
   
2. Find the run report you want to add to a project. For that run, click the gear menu on the right and select Add Report To Project :
   
   
   
   
   
   
   
   
3. The Pick Projects page opens:
   
   
   
   
   
   
   
   
4. Enable the checkbox for the project (or projects) you want the run report added to.
   
   Click the Add projects button. The run report is added to the selected project or projects.

Visit the Data > Projects > projectname page to see the analysis in the project.

Terminate an analysis run

To terminate a run that has not yet completed, go to the Services option in the Admin menu and click Terminate to the right of the run name. (See also: Terminate an Analysis Run , under Use Cases )

Change the analysis reference

Use the following procedure to change the reference for an analysis:

1. Follow the instructions in Reanalyze a run to open the run analysis dialog advanced options.
   
   
   
   
2. Use the Alignment Reference menu to select the new reference:
   
   
   
   
   
   
3. Follow the instructions in Reanalyze a run to save your selection and to redo the analysis.
   
   

Change run metadata

The Completed Runs & Reports gear menu Edit option allows you to change the metadata for a run. You use the Edit option for example, to add barcoding to a run, to change the barcode set, to add a note, or to correct the following run metadata:

• Sample name
• Application type (run type)
• Library kit
• Sequencing kit
• Chip identifying barcode
• Library key
• Notes
• Alignment reference
• Target regions BED files
• Hotspot regions BED or VCF files
• Plugins
• DNA barcode set (index)
• 3' adapter
  
  

Points to know about changing metadata:

• The run report (in the Completed Runs & Reports tab) always shows the metadata in effect for the run.If your changes are not shown in the run report, the changes were not in place at the time the report was generated.
• If you add or change an entry in the Notes field, that note does not appear in the run report unless you restart or re-analyze the run (even though the note does not affect the analysis results).

Add barcoding to a completed run

Use the Edit option to do either of the following:

• Add barcoding to a run
• Change the barcode set for a run
• Remove barcoding from a run

In each case, you must reanalyze the run after editing the barcode information. These steps apply only to completed runs.

The Edit Run page

The Edit option opens the Edit Run page:

Location of the Edit option or button

In the table view, the Edit option is found in the gear menu on the right of a run entry:

In the list view, use the Edit button on the right of the run entry:

Edit run metadata

Follow these steps to change metadata for a run:

1. In the table view, click the Edit option in the run entry's gear menu. In the list view, click the edit button in the run entry.
   
   
2. In the Edit Run page, make your corrections to the metadata.
   
   
3. When you are done, click Save .
   
   
4. Restart the run:
   
   
   1. If the run isin progress, terminate the run and restart it.
   2. If the run is completed, re-analyze the run.
      
      
      
      
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   Your changes i n the Edit Run page do not affect a run that is in progress.