When launching an analysis, BaseSpace Sequence Hub automatically aggregates all data associated with the same biosample name. For more information, see Associating Biosample Data With Projects.
To correct aggregation of data, requeue the run with a corrected biosample name. Only the run owner can requeue a run.
Edit the biosample name.
If you are using a sample sheet, useFix Sample Sheet.
If you are using the Prep tab, change the sample name in the Prep tab.
Requeue the run.
The previous run data will be marked as failed and can be deleted to reduce storage costs.
When launching apps using biosamples as inputs, BaseSpace Sequence Hub automatically aggregates all of the valid (QC Passed) biosample FASTQ data associated with the same default biosamples. You can control which data are used in analyses by setting the QC status of a resource as QC Passed or QC Failed.
Aggregated FASTQ data can be produced from multiple libraries, lanes, or flow cells, and can contain data with different read lengths from the same biosample.
To prevent unintended aggregation, biosamples are locked if the biosample was converted from a sample and has data produced by two or more runs. The data cannot be used in analysis until the biosample has been reviewed and unlocked, however you can use samples to launch analysis without aggregation. For information about unlocking biosamples to make them available for analysis, see Unlock Biosamples.
Samples contain data from a single sequencing run only, and therefore do not support data aggregation.
When BaseSpace Sequence Hub collects data for an app launch, it automatically excludes QC-failed lanes, libraries, pools, and any downstream data they produced. For example, if you fail a flow cell lane, all FASTQ data sets produced from that lane are excluded when aggregating data for the biosamples and libraries put on those lanes. If you fail a FASTQ dataset, only that FASTQ dataset is excluded.
If a FASTQ dataset has been copied, BaseSpace Sequence Hub uses the original FASTQ dataset, or the most recent copy if the original is not available. To use a different copy, mark the other copies as QC Failed before starting the analysis.
The following resources can be excluded from data aggregation:
Lanes—Fail lanes using Automatic Lane QC, BaseSpace Sequence Hub API, or manually in BaseSpace Sequence Hub.
Libraries—Fail libraries using the BaseSpace Sequence Hub API.
Pools—Fail pools using the BaseSpace Sequence Hub API.
FASTQ Datasets—Fail FASTQ data sets using the BaseSpace Sequence Hub API, or manually in BaseSpace Sequence Hub.
When using apps that have not been updated to use biosamples or data sets as inputs, BaseSpace Sequence Hub automatically converts the FASTQ data sets into samples before launching the app.
If you specify a library prep kit when selecting a biosample for analysis, the analysis launches using only FASTQ datasets from libraries of the specified prep kit. In the following example, Prep Kit B is selected as input and the FASTQ files from Prep Kit A are excluded.
Biosamples that were converted from samples are automatically locked if they contain data produced by two or more runs. To use the data for analyses, unlock the biosample. Before unlocking a Biosample, review the data to ensure accuracy.
Navigate to the Biosample summary page and select the FASTQ Datasets tab.
Review the data and identify any data that should be excluded.
To exclude data, do the following:
From the Datasets tab, select one or more datasets to exclude.
From the Status menu, point to Change, and then select FASTQ QC.
In the Change FASTQ QC Status dialog box, select QC Failed.
[Optional] Add a comment.
Select Save.
There are several ways to unlock Biosamples:
To unlock a biosample from the Biosample details page,
Navigate to the Biosample summary page.
A locked Biosample will display a red lock icon in the Biosample Status field.
From the Status menu, point to Unlock, and then select Biosample.
Select Continue.
To unlock multiple biosamples from a biosample list,
Navigate to the Biosample list page or the Project Biosamples tab.
Use the checkboxes to select Biosamples.
From the Status menu, point to Unlock, and then select Biosample.
Select Continue.
When unlocking multiple Biosamples, any selected Biosamples that are already unlocked will be ignored.
