HOW TO VISUALIZE COPY NUMBER SEGMENTS AND LOGRS IN AFFYMETRIX'S GTC BROWSER

Affymetrix provides a robust genome browser with its Genotyping Console software enabling you to visualize log2 ratios (referred to as LogRs) and copy number variations (CNVs) for each sample in your dataset. This tutorial will lead you step-by-step through exporting CNV segments and LogRs from CNAM and viewing them in Affymetrix’s GTC Browser (Figure 1).

NOTE: This tutorial can be used to visualize LogRs from any data provider not just Affymetrix.

Overview:

1. 1. Prepare a LogR DSF
2. 2. Import Affymetrix marker map
3. 3. Convert LogRs to CNT files
4. 4. Perform copy number segmentation
5. 5. Open CNT and WIG files in Affymetrix GTC Browser

REQUIREMENTS

To complete this tutorial, you will need the following:

• HelixTree
• Copy Number Analysis Module (CNAM)
• Affymetrix's Genotyping Console 2
• Sample LogR DSF file (DSF file containing 500K LogRs from four HapMap samples)

Prerequisite Knowledge:
Basic Golden Helix SVS functionality