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This user guide describes how to export copy number and genotype data using Partek's Report Plug-in for Illumina GenomeStudio Genotype Module for use in Partek Genome Suite. The GenomeStudio plug-in lets you export data into a project that can be opened in Partek Genome Suite open directly. It is the fastest and most consistent way to get fully annotated Illumina gene expression data into Partek.
Partek Genotype plug-in installation
Download the plug-in zip file, unzip the file, there is a folder called PartekReport which contains two .dll files --Partek.Common.dll and Partek.GeneExpression.GenomeStudio.dll, move the PartekReport folder to
C:\Program Files \Illumina\GenomeStudio 2.0\Modules\BSGT\ReportPlugins, if there is no ReportPlugins folder in BSGT folder, create one, the path and folder names have to be exactly match one described above (Figure 1).
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Export report from GenomeStudio
In GenomeStudio genotype project:
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Open project in Partek Genomics Suite
To open the report, launch Partek Genomics Suite, choose File > Open Project, browse to the .ppj file to open. There will be three spreadsheets opened (Figure 4)
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