Manual QC

In some cases, you might need to override a QC status that was automatically set by BaseSpace Sequence Hub. When a resource is set to QC failed, its data and any data produced from it are excluded from downstream data analyses and total yield calculations. For more information about excluding data from analyses, see Automatic Data Aggregation.

Changing the QC status of a resource does not change the QC status of downstream resources produced from it.

You can fail Lanes, Libraries, Pools, and FASTQ Datasets using the API. For more information, see the developer documentation at developer.basespace.illumina.com.

Change Lane QC Status

For information about automatic lane QC, see Automatic Lane QC.

1. Open the Run & Lane Metrics page for the desired run.

   1. Select the Runs tab.

   2. From the Runs list, select a run.

   3. From the Run Summary page, select the Run & Lane Metrics icon

2. Select one or more lanes that have the same QC status.

3. Select the Status drop-down arrow, point to Change, and then select Run Lane QC.

4. In the Change Lane Status dialog, review the selected lanes and do the following:

   1. Select the Change Status to drop-down arrow and then select a new status, QC Passed or QC Failed.

   2. [Optional] Add a comment.

Change FASTQ QC Status

You can change the status of a generated or uploaded FASTQ dataset.

1. Open the Output Files tab for the desired biosample.

   1. Select Biosamples.

   2. From the Biosamples master list, select a biosample.

   3. From the Biosample Details page, select the Output Files tab.

2. Select one or more FASTQ data sets that have the same QC status.

3. Select the Status drop-down arrow, point to Change, and then select FASTQ QC.

4. In the Change FASTQ QC Status dialog, review the selected FASTQ data sets and do the following:

   1. Select the Change Status to drop-down arrow and then select a new status, QC Passed or QC Failed.

   2. [Optional] Add a comment.

Change Analysis QC Status

You can change the status of analyses that have completed. Changing the analysis QC does not affect the QC of the FASTQ data sets.

1. Select Analyses to open the Analyses master list.

2. Select one or more analysis workflows that have the same QC status.

3. Select the Status drop-down arrow, point to Change, and then select Analysis QC.

4. In the Change Analysis Status dialog, review the selected analyses and do the following:

   1. Select the Change Status to drop-down arrow and then select a new status.

   2. QC Passed—All analysis data sets passed QC.

   3. QC Failed—One or more analysis data sets failed QC.

   4. Discarded—The QC-failed analysis has been reviewed and can be ignored.

   5. [Optional] Add a comment.