|Extracting Data from GenomeStudio Using the Golden Helix DSF Export Plug-in
In collaboration with Illumina, Golden Helix has developed a set of custom plug-ins to streamline the transfer of genotype, log ratio and bookmark files between Golden Helix's SNP & Variation Suite (SVS) applications and Illumina's GenomeStudio Data Analysis software. These instructions lead you through extracting genotype and log ratio data from GenomeStudio as a Golden Helix DSF file and importing the DSF file into SVS version 7 and 6 (a.k.a HelixTree 6).
Before beginning the installation process, make sure all instances of GenomeStudio are not running.
Open the Golden Helix GenomeStudio DSF Plugin-3.0.exe file and follow the instructions in the installation wizard. Upon completion of the wizard, three plug-ins, including the Golden Helix DSF Export plug-in, will be extracted to the appropriate GenomeStudio folders. By default these folders are located in C:\Program Files\Illumina\GenomeStudio\.
Extracting Data from GenomeStudio
If the installation was performed successfully, the Golden Helix DSF Export Plug-in can be accessed from an open project in GenomeStudio using the Report Wizard. The following instructions will guide you through this process.
Open a GenomeStudio project and select Analysis >Reports >Report Wizard.
From the first window of the wizard choose Custom Report and then select Golden Helix DSF Export 3.0 from Golden Helix, Inc. (below). Click Next to continue.
The next window asks which samples you would like to include in your report. Select the appropriate sample set and click Next.
If you have multiple sample groups in your project you will be asked to select the ones you want to export. Select the sample groups and click Next.
On the following window Browse to an appropriate directory where you want the resulting DSF file to be saved. Give the report a name and click Finish.
This will activate the Golden Helix DSF Export Plug-in, opening the following window:
Chromosomes to Export: By default all the chromosomes represented in your project are listed. If you only want to export a subset of chromosomes click Pick Chromosomes and check the chromosomes you want to export.
Output for Compatibility With: The DSF file format created for use in SVS v7 is slightly different than that for v6 as well as provides the ability to include marker map information. Choose the output format according to which version of the software you plan on importing the resulting DSF file into.
Data to Export: Choose whether you want to export SNP call data or log ratio data for copy number analysis. If you choose HelixTree 6 you can pick which strand you want to export. Choosing SVS 7 does not give this option as you can use the resulting embedded marker map info to post convert alleles among the three strands.
Data Orientation: If you selected the output to be compatible with SVS 7 you have the choice top orient the data where samples are rows or columns. There are advantages/disadvantages of both. If you are exporting log ratio data, orienting samples as columns will be faster than orienting as rows. It also provides and efficient means to visualize log ratio data in the genome browser provided in SVS 7 as the browser can only plot columns in a spreadsheet. However, if you want to run CNAM Optimal Segmenting or association analysis on the log ratio data, you will need to transpose the data once it is imported into SVS 7. The overall efficiency of exporting, importing, and transposing will depend on the size of the dataset.
There is no speed advantage when exporting SNP data where samples are columns, so it is recommended you choose to orient samples as rows.
Upon completion a DSF file will be created in the directory location you chose.
Importing DSF File into SVS 7
The method for importing an Illumina DSF is the same for both log ratio and SNP calls.
From an open project select Import >Illumina DSF.
When the import is complete, a dialog box will appear asking if you would like to save the marker map included with the DSF file to your permanent MarkerMaps folder for use on a different dataset. Click Yes if you want to save the included marker map and No if you don’t.
Importing DSF File into HelixTree 6
The method used to import data into HelixTree 6 depends on whether you selected to export SNP call data or log ratios.
SNP Call Data
From an open project select File >Import Data >Import DSF.
When the import is complete, a dialog box will appear letting you know that your file included base pairs in the A,B format. Click Yes if you want to convert it to standard genetic base pairs or No if you want keep the existing format.
Log R Ratios Data
There are several analysis operation you can perform directly on the output LogR DSF file: import the LogR data as a spreadsheet, perform logR association tests, or perform CNAM optimal segmenting the LogR Data.