Genes in gtf or gff format

UCSC does not keep gene structures in GTF format, we use a single line format for a single gene with all the information about that gene in the single line: GenePred format.

Extracting GTF format files from the genePred format can be performed with the genePredToGtf:

kent command utility.

At this time, this genePredToGtf command can provide better GTF files than available from the table browser.

To use the kent commands, add this three line file ".hg.conf" to your home directory:

$ cat $HOME/.hg.conf
db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password

And set the permissions:

$ chmod 600 .hg.conf

Now you can use the command to extract GTF files directly from the UCSC database. For example, fetch the UCSC gene track from hg19 into the local file knownGene.gtf:

$ genePredToGtf hg19 knownGene knownGene.gtf

Note the usage message from the command:

enePredToGtf - Convert genePred table or file to gtf.
usage:
    genePredToGtf database genePredTable output.gtf
If database is 'file' then track is interpreted as a file
rather than a table in database.
options:
   -utr - Add 5UTR and 3UTR features
   -honorCdsStat - use cdsStartStat/cdsEndStat when defining start/end
    codon records
   -source=src set source name to uses
   -addComments - Add comments before each set of transcript records.
    allows for easier visual inspection
Note: use refFlat or extended genePred table to include geneName

You can also fetch the database text dump of the genePred content for the track to have the file on-hand locally:

ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz The SQL structure: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql

As noted in the usage message, the file can be used with the command in place of the database table specification.