Analysis Setup
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Before beginning analysis, ensure workgroup context is being used so analysis can be viewed by all members of your workgroup. The name of your workgroup should appear in the top right corner.
Use the following steps to run the Microarray Analysis Setup on BaseSpace Sequence Hub:
Select the Runs tab
Select New Run
Select Microarray Analysis Setup
Enter the Analysis Name (Figure 1)
Use the Select Project link to choose the project for your output files To select an existing project, click the radio button next to the desired project name. You can also create a project by clicking the New button in the project selection window.
Select the Type of Analysis Further detail of each Type of Analysis is available in and
(Optional) Create a custom configuration via the "Add Custom Configuration" option in Configuration Settings. Custom configurations must be assigned a name and product files can be uploaded or selected (Figure 2). Custom configuration options vary by Type of Analysis including:
DRAGEN Array - Genotyping provides flexibility for turning off/on specific output files and adjusting GenCall score cutoff. Its recommended to turn off VCF output for non-human species and Final Report output for large sample numbers.
DRAGEN Array - Methylation - QC provides options to adjust thresholds as detailed in section DRAGEN Array Methylation QC .
Select your preferred option in the Configuration Settings drop-down menu Configuration setup will vary based on the Type of Analysis selected. More details are available in section .
Select Next
Select either Import Sample Sheet, Select BeadChips, or Import IDAT Files (Figure 3)
Import Sample Sheet presents a link to upload sample sheet. Users may download a template sample sheet by selecting the Download Template link.
Select BeadChips allows users to select BeadChips from the displayed list of available BeadChips. If selecting specific samples within the BeadChip is desired the Import Sample Sheet option should be used.
Import IDAT Files allows users to upload the IDAT files from a local folder to the cloud platform for use with the current and future analyses by users within the same workgroup.
Select Launch Analysis
On the Analyses tab, view the analysis status, e.g., initializing or complete.
After the analysis is complete, select the analysis and select the Files tab.
From the Files tab, select the Output folder.
There are background processes necessary for analysis that run after the IDAT upload session has completed. In most cases these processes should take a few minutes at most after which you may launch analysis. If after some time there are samples that are still not marked ready for analysis, try re-importing the IDATs for the affected samples. If the issue persists, please contact Illumina Tech Support at techsupport@illumina.com.
The system requires a product association for every BeadChip. Please ensure that the product associated with the selected analysis configuration is also associated with the IDATs selected for import. Mismatch between the IDAT product identity and the analysis configuration selected may affect the ability to select samples for analysis. Contact techsupport@illumina.com to resolve product mismatch issues.
There is an idle timeout that may take effect for longer uploads. This means that if you are inactive for more than the set timeout duration you will be automatically logged out and file upload will stop.
To avoid any interruption with the file upload, we recommend that you stay active on the page while your file is uploading. Alternatively, if you plan on uploading large amount of samples at a time, we suggest breaking your upload into multiple batches to avoid hitting the timeout.
The best way to check the import status is to go to the page.
The timeout duration may be configured for enterprise domains by following the steps found in .
