Change the Default Alignment Reference

Use the following procedure to change the default alignment reference for an analysis.

In the Data tab, click Completed Runs & Reports.
Click Table View.
Navigate to your run of interest.
See Search for a run for help finding an individual run.
For that run, click Settings () > Reanalyze.
In the Reanalysis screen for the run, click Reference & Barcoding.
Select a new reference from the Default Alignment Reference menu.

Note:
If various references were selected per barcode in the first run, use the lower per-barcode reference selection utility here as well.
Follow the instructions in Reanalyze a run to save your selection and to redo the analysis.