# 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="<https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-6247021ccf7eb009f9713d971d8c5ae00d93a587%2FPartekReportGX.zip?alt=media&token=b13cbd5f-6e52-40b3-843e-6b545a632fda>" %}

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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-e535de6c6c4e729a8b30fddeeb5ed5712f6455d6%2FGT%20dialog.png?alt=media)

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)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a2cc6f9fa9d943049243123f77bd48bc0fc3ffbc%2Foutput%20dialog.png?alt=media)

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)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-47cc4c8b17ad34c7622ba57516eb963e77354e97%2Fpgs%20project.png?alt=media)

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.