5. Open CNT and WIG files in Affymetrix GTC Browser

Now that you have created WIG and CNT files for each sample, you can open them with Affymetrix’s GTC Browser. This browser comes standard with Affymetrix’s Genotyping Console, a program freely available for anyone who has a registered Affymetrix login and password.

If you do not have Genotyping Console installed, you can Download and Install Genotyping Console here:

http://www.affymetrix.com/products/software/specific/genotyping_console_software.affx

NOTE: This tutorial will focus on very basic functionality of the GTC Browser. For more information refer to the manuals included in the download link above.

Once Genotyping Console is installed, the GTC Browser will appear in the Affymetrix folder. Windows users can access this program by going to >Start >All Programs >Affymetrix >GTC Browser.

Open the GTC Browser. The window in Figure 1 will appear.

NOTE: If the Annotation Types are selected, uncheck them.

To open the CNT files containing LogRs select >File >Open. Navigate to the folder where you saved the CNT files in Step 3. You can select multiple files by holding down the Shift key. Once the files are selected, click Open.

Four samples will appear in the top left of the window (Figure 2). To view the LogRs for these files you will need to view Chromosome 22 by selecting >View >Display Chromosome >22. LogRs will now be visible for each sample (Figure 3).

To view the copy number segmenting results for these samples go to >File >Open, navigate to the directory containing the WIG files output in Step 4, Shift Click to select all four files and click Open.

The segmenting results will appear below the LogRs (Figure 4). From here you can move samples around, choose to view only selected samples at a time, zoom in, change graph properties, etc. (Figure 5 shows only LogRs and segments for CEU_NA06985). Other options enable you to view specific segments in public genome browsers (UCSC, Ensembl, Toronto).