Process Description

Track Gene GFF

The Track Gene GFF process uses a GFF text file as input to create a text file and accompanying Track Gene Text settings (.sas) file that defines a track for genes. The settings file can then be selected as a track file for embellishing graphics with depictions of genes.

What do I need?

A single .gff input file, which contains track information, is required. The TAIR9_GFF3_genes.gff file (downloaded from The Arabidopsis Information Resource website (http://www.arabidopsis.org/), saved to the JMP Genomics Sample Data\GFF directory, and shipped with JMP Genomics) serves as an example.

The input file must have nine columns, in the correct order, to properly define the genomics features. This file must be tab delimited. Data can begin on the first row, or the first row after any comment lines, which must begin with "##".

Required columns are listed in the following table.

Column Order	Column	Description
1	seqname	Values in this column define the name of the sequence (Chr1, for example); values must represent either a chromosome or scaffold.
2	source	Values in this column define the program that generated this feature.
3	feature	Values in this column define the name (examples include gene, mRNA, protein, start_codon, stop_codon, and three_prime_UTR) of this type of feature.
4	start	Lists the starting position of the feature in the sequence. The first base is numbered 1.
5	end	Lists the ending position of the feature (inclusive).
6	score	A score between 0 and 1000, which determines the level of gray in which this feature is displayed (higher numbers = darker gray).
7	strand	Lists the strand orientation of the feature. Valid entries include “+” for the plus strand, “-” for the minus strand, or “.” if the orientation is not known.
8	frame	If the feature is a coding exon, the frame should be some number between 0 and 2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be “.”.
9	group	All lines with the same group are linked together into a single item.

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

Output/Results

Running the Track Gene GFF process results in the generation of a setting file (for example, TrackGeneText_Arabidopsis.sas), whose path is displayed in the JMP Genomics Message window.

If opened in SAS, code resembling the following is seen.

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