Launch Analysis
Running Analysis
This page describes how to start an analysis immediately using data that has already been scanned and uploaded. To access this workflow, navigate to the Microarray Hub, select the Data Management tab, and select Start an analysis.
If you want to set up an analysis before your samples have been scanned, see Planned Analyses to create an analysis that will auto-launch when sample data becomes available.
Use the following steps to configure and launch an analysis:
Enter the Analysis Name
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 DRAGEN Array Applications and Polygenic Risk Score Software
(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. Details on file name constraints can be found in the ICA documentation. Custom configuration options vary by Type of Analysis selected. More details are available in section DRAGEN Array Applications.
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 DRAGEN Array Applications.
Select Next
Select either Import Sample Sheet, Select BeadChips, or Import IDAT Files
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
View Outputs
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.
Troubleshooting IDAT Import
Checking Import Status
The best way to check the import status is to go to the Data Management page.
Sample is Not Ready For Analysis
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 [email protected].
Product Mismatch
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 [email protected] to resolve product mismatch issues.
Upload Timeout
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 timeout duration may be configured for enterprise domains by following the steps found in Session Management.
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