Step 8. Visualize Segmenting Results

There are tools available outside HelixTree to visualize your copy number segmenting analysis results. Using the optional wiggle track file output in Step 5 you can view your segmenting results using UCSC’s Genome Browser or Affymetrix’sGenome Browser. If you are analyzing Illumina data you can output the Segment Means spreadsheet created in Step 5 as a bookmark CSV file to view your results in Illumina’s BeadStudio Genome Browser.

This tutorial will cover importing data into UCSC’s Genome Browser. For a tutorial on how to visualize segmenting results in Affymetrix's GTC Browser click here. For more information on other browsers see the manual.

The UCSC Genome Browser is an online tool created by the University of California, Santa Cruz (http://genome.ucsc.edu/ cgi-bin/hgGateway), used to view genome data formatted in the Wiggle track format (WIG).

To import copy number variation analysis results in the UCSC Genome Browser, first go to the website address above. Select the add custom tracks button to open the add custom tracks page. From this page browse for the WIG file created in Step 5 and select Submit. The next page will have a table to view the tracks found in the specified WIG file. To add more data tracks (samples), select add custom tracks. To view the tracks in the genome browser (Figure 1), select go to genome browser.

NOTE: There are some restrictions on the data that can be imported into the UCSC Genome Browser because it is an online tool. When performing multivariate segmenting analysis in CNAM, the results may contain segments that are only one marker in length. The UCSC Genome Browser does not accept data files containing segments with length equal to one. To avoid this conflict, in Step 5 set the Min #Markers per segment parameter in the Copy Number Segmentation tool to a value greater than one.

The second conflict when using the USCS Genome Browser to view CNAM segmenting results occurs when the difference between a segment’s chromosome start position and chromosome end position is found to be larger than 10,000,000 bp. Currently the best way to handle this issue is to manually separate the large segments into multiple adjacent segments with the same segment mean. The WIG file can be opened and edited in a text editor. Following the format outputted by CNAM, insert rows to divide the long segment into multiple shorter segments.