How to edit sample indexes in BaseSpace Sequence Hub PrepTab

If an incorrect index was chosen during run setup on BaseSpace, MiniSeq or NextSeq 500/550 run owners can correct it in PrepTab and requeue the analysis. The troubleshooting demultiplexing issues bulletin covers how to determine if an incorrect designation occurred, and explains how to identify the correct index sequence. This bulletin explains how to edit the sample sheet to correct an incorrect index assignment.

Important Notes:

• Only changes within the same library prep kit are allowed in BaseSpace Sequence Hub. If adding an index from a different library prep kit, or selecting a different library prep kit, use bcl2fastq to do FASTQ generation offline.

• Only the original owner of the run has the ability to make edits and requeue a run. If run ownership is transferred, the original run setup, pools, and libraries associated with the run in PrepTab remain with the original owner. To make changes to a transferred run, return ownership to the original owner. Users with shared access to the run are not able to edit the PrepTab information and requeue analysis.

• If the output is set to the original project, duplicate samples and new FASTQ files are generated. New samples are distinguished from the originals only by the date stamp. To direct the revised sample data to a new project instead, first create a new project.

1. Log in to BaseSpace Sequence Hub and select the Prep tab.

2. Select Pools.
3. Select the Pool ID link that contains the sample you wish to edit. Note: The Pool ID for a given run is found on the Run Settings page: from the RUNS tab, select the run name and select the scroll icon. The Pool ID(s) are listed at the bottom of the page.
4. For the sample you wish to edit, select the Plate ID link.
5. On the Prep Libraries page, select Edit.
6. Select the checkbox for the sample you wish to edit. To change the index associated with the sample, select either the row or column designations (grey boxes). Note: The run must conform to a 96-well plate format so the same index is used down a column or across a row. Changes to the selected index affect all samples in the column or row, and the well assignment cannot be changed. To change where the new files are sent: Select the samples to send to the new project, select Set Project, and navigate to the project created in Step 1.
7. When all edits have been made, select Save. Navigate back to the original run page.

8. Requeue Analysis. Note: There are two modes of data aggregation in BaseSpace Sequence Hub: Classic and New. Instructions for requeuing are provided below for both modes. To determine which mode is being used or to switch between modes, use the toggle switch in the upper right corner of the dashboard page.

   1. If using the Classic mode of BaseSpace Sequence Hub: from the Run Summary page, select More, and choose Regenerate FASTQ. Then select Requeue to start the analysis.
   2. If using the New BaseSpace Sequence mode: navigate to the Run Summary page (select the MY DATA tab and then Runs). Select the Status icon, then Requeue and FASTQ Generation from the drop-down menus. Select Requeue to start the analysis.

The status on the run summary page displays Analyzing when the analysis is ongoing, and changes to Complete when the requeued analysis is complete.

For any feedback or questions regarding this article (Illumina Knowledge Article #1322), contact Illumina Technical Support [e-mail].