Track Gene Text

The Track Gene Text process creates a settings (.sas) file from a text file that defines a display track for a set of genes to be added to JMP Genomics statistical results like plots of -log10(p-values) along chromosome. You can download the text file from sources like the Table Browser of the UCSC Genome Browser and use it as input to this process. The resulting settings file can then be selected as a track file for embellishing graphics with depictions of genes.

What do I need?

A single .txt input file, which contains track information, is required. The hg18_knownGene.txt file serves as an example, and is shown below. This file, which was downloaded from the UCSC Table Browser to the JMP Genomics Sample Data\UCSC\Gene directory, is shipped with JMP Genomics.

The input file must have certain columns in order to properly define the genes. Columns must list:

•	gene names,

•	chromosomal location,

•	strand orientation,

•	transcription start and stop site,

•	the number of exons,

•	the 5’ and 3’ ends of each exon, and

•	the start and stop codon sites.

The file must meet the following requirements:

•	it is tab delimited,

•	its first row contains column headings, and

•	data begins on the second row.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

Output/Results

Running the Track Gene Text process results in the generation of the TrackGeneText_UCSC_hg18_known_Genes.sas settings file, whose path is displayed in a JMP Genomics Message window.

Opening the file with a text editor reveals the SAS code shown below.

This file can be used with any JMP Genomics process having a Tracks tab.