Output Description

UCSC Genome Browser

Running this process for the UCSC_Chrom_Pos_example sample setting generates an html document containing links to the UCSC genome browser for each position in the data set. Refer to the UCSC Genome Browser Link process description for more information.

The html file generated in this example is shown below:

Since Chromosome and Position were selected as variables to retain in the .html table, the position of each probeset on chromosome 1 is given, along with links to the appropriate location in the genome browser. Clicking on any of the links takes you to the UCSC genome browser.

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Click one of the links to open a UCSC Genome Browser session for the SNP at the selected position.

Selecting the link circled above opens the following UCSC Genome Browser session:

Refer to the UCSC Genome Browser documentation for more information.

You can run the UCSC Genome Browser Link process multiple times and choose additional quantitative variables for upload to the browser as separate tracks, such as fold changes, -log10(p-value), or test statistics from association. By uploading, managing, and viewing multiple custom tracks within the UCSC Genome Browser, you can link diverse data types to chromosomal positions and look for interesting trends. A number of additional custom tracks are also publicly available to users of the UCSC Genome Browser that offer further options for placing analysis results into chromosomal and biological context.