This section will guide you through the export of your genotype data from Illumnia BeadStudio into the Final Report text format and then the import of that data in to HelixTree using the Import Illumina Exported From BeadStudio script.

For users of Beadstudio 3.0 or greater, you may also use the DSF plug-in to export a DSF of genotype data. For details about this type of export, see section D.3.

D.2.1 Exporting the Data from BeadStudio

Begin by opening a BeadStudio Project. In the BeadStudio window select from the menu bar Analysis->Reports->Reports Wizard.

Figure D.1: The Illumina BeadStudio window with the Analysis and Reports menus expanded.

Select in the Reports Wizard Final Report and click Next.

Figure D.2: Selecting the report type in the BeadStudio Reports Wizard

Select the sample groups to be included in the report and click Next. The next screen will ask you how you would like to format your final report. Make sure that you choose Group by SNP. You may select to either export as a comma delimited or tab delimited file. For the Displayed Fields list, HelixTree will only recognize either the defaults shown or some variation of Allele1 and Allele2 (i.e. Allele1 - Top, Allele1 - Forward, Allele1 - Design). Therefore, it is not necessary to include additional available fields in the report. The Displayed Fields list must be in the default order as shown below. If you wish to associate a marker map with your data, then you will also want to check the Create map files box. When you are finished selecting the proper parameters, click Next.

Figure D.3: Selecting final report format

Select the output path and file name and click Finish.

Figure D.4: Setting the Output Path and the Report Name in the BeadStudio Reports Wizard

D.2.2 Importing the Data into Helixtree

To import the Final Report text file into HelixTree, first open a project in HelixTree. From the Project Navigator select File->Import Scripts->Import Illumina Exported From BeadStudio.

Figure D.5: Opening the Import Illumina Data Exported From BeadStudio script

Select the Final Report file that you exported from BeadStudio and click Open. A dialog box will appear asking for the file type and whether you want to use a GC Score. Using the GC Score will convert genotype calls into missing values if they do not meet a user-specified threshold. Choose your parameters and click OK.

Figure D.6: Selecting import parameters for Illumina text file import

If you chose to use a GC Score threshold, a second dialogue box will appear asking you to enter that threshold. Input your GC Score threshold and click OK.

Figure D.7: Selecting GC Score for Illumina text file import

HelixTree will then import your data. Once the import is complete, a message will appear with some import statistics. These statistics will also be recorded in the Annotation Window within the Project Navigator.