# Import Genotype Data

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

{% file src="/files/GnX2LhMCg0GmWcLlke09" %}

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).

## Export report from GenomeStudio

In GenomeStudio genotype project:

* Choose **Analysis > Reports>Report Wizard** from the main menu
* Select **Custom Report** and choose **Partek Report Plug-in** from the drop-down list
* Specify *AnnotationName*, do NOT include **<>** in the name, you can the same name as the .bgx file you imported the ddata with, or a unique name to your dataset

![](/files/DcCmzqzDS4YGEnGLTMvF)

Figure 1. Configuring the GenomeStudio copy number report dialog

* Leave all the others as default value (Figure 2) click **Next**
* Specify the report file name, we recoommend to put the exported files in their own folder, which allows you to move thefolder instead of all the files individually.
* Click **Finish** (Figure 2)

![](/files/dKE1exCN9udHEKnF20X6)

Figure 2. Specify output folder and file name

The output generate 9 files in the folder including a project file (.ppj), annotation file, summary file and 3 sets of Partek spreadshet file-- each spreadsheet consists of 2 files.

## 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 3)

![](/files/IZ8dF1hVgm1DEOkHQ3B7)

Figure 3. Open project in Partek Genomics Suite

Spreadsheet 1 contains genotype calls, spreadsheet 2 contains log R ratio which is copy number in log scale, spreadsheet 3 contains B allele frequency.

To do copy number analysis, select spreadsheet 2 log R ratio, choose Copy number workflow, start from QA/QC section. Genotype spreadsheet will be used for Association and LOH workflow.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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