Analysis Setup
Running Analysis
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)
Figure 1. Configuration step of Microarray Analysis Setup 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 (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 Threshold Adjustment.
Figure 2. Optional Custom Configuration step of Microarray Analysis Setup 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 (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
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.
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