Genes in gtf or gff format (original) (raw)

GTF Downloads Directory

Summary of limitations for Table Browser GTF output

Warning - using a non genePred table to get GTF output in the Table Browser

A genePred table (such as knownGene) is needed to get GTF output in the Table Browser. Below is an example of output for the knownCanonical table, which is NOT in genePred format. Even though the TB GTF says "exons" for knownCanonical GTF output, it's really just a placeholder, not exons at all, but rather start-stop regions of the transcripts.

For example, if you do a cart reset (top menu > Genome Browser > Reset All User Settings) and go to the default region (chr1:11102837-11267747) in hg38, then go to the Table Browser, and then get all fields for knownCanonical (limit to default region, not genome), you'll get this output:

#chrom chromStart chromEnd clusterId transcript protein chr1 11106534 11262507 17297 uc001asd.4 ENSG00000198793.12 chr1 11143897 11149537 24285 uc031plf.2 ENSG00000225602.5 chr1 11152349 11152452 33500 uc057cga.1 ENSG00000253086.1 chr1 11189340 11195981 13013 uc001ase.5 ENSG00000171819.4 chr1 11226253 11226360 20530 uc057cgc.1 ENSG00000207451.1

GTF output for that same region will be:

chr1 hg38_knownCanonical exon 11106535 11262507 0.000000 . . gene_id "gene1"; transcript_id "tx1"; chr1 hg38_knownCanonical exon 11143898 11149537 0.000000 . . gene_id "gene2"; transcript_id "tx2"; chr1 hg38_knownCanonical exon 11152350 11152452 0.000000 . . gene_id "gene3"; transcript_id "tx3"; chr1 hg38_knownCanonical exon 11189341 11195981 0.000000 . . gene_id "gene4"; transcript_id "tx4"; chr1 hg38_knownCanonical exon 11226254 11226360 0.000000 . . gene_id "gene5"; transcript_id "tx5";

Note that the GTF regions are not exon regions, they are start-stop regions. Note also that GTF is 1-based, unlike 0-based "all fields" output. See the coordinate blog for more information about 0-based vs 1-based coord systems.

Example: Comparing Table Browser GTF output with genePredToGtf utility output

Table Browser output for ENST00000376819.3.

chr1 hg38_wgEncodeGencodeBasicV26 start_codon 11189580 11189582 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 CDS 11189580 11189955 0.000000 + 0 gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 exon 11189341 11189955 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 CDS 11192270 11192370 0.000000 + 2 gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 exon 11192270 11192370 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 CDS 11193580 11193774 0.000000 + 0 gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 exon 11193580 11193774 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 CDS 11194461 11194659 0.000000 + 0 gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 exon 11194461 11194659 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 CDS 11194854 11195020 0.000000 + 2 gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 stop_codon 11195021 11195023 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3"; chr1 hg38_wgEncodeGencodeBasicV26 exon 11194854 11195981 0.000000 + . gene_id "ENST00000376819.3"; transcript_id "ENST00000376819.3";

genePredToGtf utility output

$ genePredToGtf hg38 wgEncodeGencodeBasicV26 utilityOutputBasic26.gtf

$ cat utilityOutputBasic26.gtf| grep -w ENST00000376819.3

chr1 wgEncodeGencodeBasicV26 transcript 11189341 11195981 . + . gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 exon 11189341 11189955 . + . gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "1"; exon_id "ENST00000376819.3.1"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 CDS 11189580 11189955 . + 0 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "1"; exon_id "ENST00000376819.3.1"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 exon 11192270 11192370 . + . gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "2"; exon_id "ENST00000376819.3.2"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 CDS 11192270 11192370 . + 2 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "2"; exon_id "ENST00000376819.3.2"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 exon 11193580 11193774 . + . gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "3"; exon_id "ENST00000376819.3.3"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 CDS 11193580 11193774 . + 0 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "3"; exon_id "ENST00000376819.3.3"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 exon 11194461 11194659 . + . gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "4"; exon_id "ENST00000376819.3.4"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 CDS 11194461 11194659 . + 0 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "4"; exon_id "ENST00000376819.3.4"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 exon 11194854 11195981 . + . gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "5"; exon_id "ENST00000376819.3.5"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 CDS 11194854 11195020 . + 2 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "5"; exon_id "ENST00000376819.3.5"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 start_codon 11189580 11189582 . + 0 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "1"; exon_id "ENST00000376819.3.1"; gene_name "ANGPTL7"; chr1 wgEncodeGencodeBasicV26 stop_codon 11195021 11195023 . + 0 gene_id "ANGPTL7"; transcript_id "ENST00000376819.3"; exon_number "5"; exon_id "ENST00000376819.3.5"; gene_name "ANGPTL7";

Convert genePred to GTF with the genePredToGtf command line utility

GenePred is a table format commonly used for gene prediction tracks in the UCSC Genome Browser. The genePredToGtf command-line utility can be used to convert genePred to GTF.

While the Table Browser does contain an option to output query results in GTF, the output is limited, and in some cases, may contain bugs. The best method to convert genePred to GTF is the genePredToGtf command-line utility. The operating-specific utility can be downloaded from the utilities directory.

Once downloaded (and permissions changed to executable), you can run the utility without arguments to see the usage statement:

$ genePredToGtf genePredToGtf - 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 use -addComments - Add comments before each set of transcript records. allows for easier visual inspection Note: use a refFlat table or extended genePred table or file to include the gene_name attribute in the output. This will not work with a refFlat table dump file. If you are using a genePred file that starts with a numeric bin column, drop it using the UNIX cut command: cut -f 2- in.gp | genePredToGtf file stdin out.gp

Using Table Browser output as input for the genePredToGtf

You can use Table Browser output as input for the genePredToGtf utility, but you will need to check that the Table Browser output is indeed in the correct GenPred format. In some cases, you may have trailing columns that need to be removed.

For example,

  1. From the UCSC Genome Browser, click on "Genome Browser" at the top menu bar, then select "Reset All User Settings" to refresh to the default hg38 assembly and its default position.
  2. Go to the Table Browser, and keeping all options as default, change only 1 setting: region should be set to "position" instead of genome.
  3. Accept the default drop-down option for "output format" as "all fields from selected table" and
  4. Type in a name for "output file" to download your file (e.g., "knownGeneABO.txt").
  5. Click "get output."

Note that you will have 12 columns; and you will need to remove the last two columns to get genePred format:

cat knownGeneABO.txt | cut -f1-10 > knownGeneABO.genePred

Now convert to GTF, using the "file" argument for genePredToGTF:

genePredToGtf file knownGeneABO.genePred knownGeneABO.gtf

Use genePredToGtf with a downloaded genePred table

You can directly download a table (for example, the knownGene table), which will be in genePred format. You can then use this local file as input for the genePredToGtf conversion.

ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz

The SQL structure:

ftp://hgdownload.soe.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. In this case, beware of files that are only partially genePred format. For example, the knownGene.txt.gz file has extra columns after the exonEnds column. Therefore, use cut to extract just the columns for genePred:

$ zcat knownGene.txt.gz | cut -f1-10 | genePredToGtf file stdin knownGene.gtf

Example with downloaded refGene.txt.gz

Here are detailed steps for converting a local hg19 refGene table (in genePred format) to GTF.

1. Download your gene set of interest for hg19. For this example, I'll use the refGene table, but you can choose other gene sets, such as the knownGene table from the "UCSC Genes" track.

rsync -a -P rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ./

2. Unzip

gzip -d refGene.txt.gz

3. Remove the first "bin" column:

cut -f 2- refGene.txt > refGene.input

4. Convert to gtf:

genePredToGtf file refGene.input hg19refGene.gtf

5. Sort output by chromosome and coordinate

cat hg19refGene.gtf | sort -k1,1 -k4,4n > hg19refGene.gtf.sorted

Example output for hg19refGene.gtf.sorted:

$head hg19refGene.gtf.sorted chr1 refGene.input exon 10002682 10002840 . - . gene_id "LZIC"; transcript_id "NM_001316973"; exon_number "7"; exon_id "NM_001316973.7"; gene_name "LZIC"; chr1 refGene.input exon 10002682 10002840 . - . gene_id "LZIC"; transcript_id "NM_001316975"; exon_number "7"; exon_id "NM_001316975.7"; gene_name "LZIC"; chr1 refGene.input exon 10002682 10002840 . - . gene_id "LZIC"; transcript_id "NM_001316976"; exon_number "5"; exon_id "NM_001316976.5"; gene_name "LZIC"; chr1 refGene.input exon 10002682 10002840 . - . gene_id "LZIC"; transcript_id "NM_032368"; exon_number "7"; exon_id "NM_032368.7"; gene_name "LZIC"; chr1 refGene.input CDS 10002739 10002793 . - 0 gene_id "LZIC"; transcript_id "NM_001316974"; exon_number "7"; exon_id "NM_001316974.7"; gene_name "LZIC"; chr1 refGene.input exon 10002739 10002840 . - . gene_id "LZIC"; transcript_id "NM_001316974"; exon_number "7"; exon_id "NM_001316974.7"; gene_name "LZIC"; chr1 refGene.input start_codon 10002791 10002793 . - 0 gene_id "LZIC"; transcript_id "NM_001316974"; exon_number "7"; exon_id "NM_001316974.7"; gene_name "LZIC"; chr1 refGene.input exon 10002981 10003083 . + . gene_id "NMNAT1"; transcript_id "NM_001297778"; exon_number "1"; exon_id "NM_001297778.1"; gene_name "NMNAT1"; chr1 refGene.input transcript 10002981 10045556 . + . gene_id "NMNAT1"; transcript_id "NM_001297778"; gene_name "NMNAT1"; chr1 refGene.input exon 10003307 10003485 . - . gene_id "LZIC"; transcript_id "NM_032368"; exon_number "8"; exon_id "NM_032368.8"; gene_name "LZIC";

Using kent commands with the public database server

To use the kent commands with the public database server, add this four line file ".hg.conf" to your home directory. One way is to use the echo command and the >> to append lines into .hg.conf:

echo db.host=genome-mysql.soe.ucsc.edu >> .hg.conf echo db.user=genomep >> .hg.conf echo db.password=password >> .hg.conf echo central.db=hgcentral >> .hg.conf

Check your work with the following command:

cat $HOME/.hg.conf

Download GenePredToGtf utility from the command line:

#for MacOSX wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/genePredToGtf #for Linux wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf

Set the permissions:

chmod 600 .hg.conf chmod +x genePredToGtf

Now you can use the genePredToGtf command to pull gene files directly from the UCSC public database and convert them to GTF format. For example, fetch NCBI's refGene track from hg38 and save to a local file named refGene.gtf:

./genePredToGtf hg38 refGene refGene.gtf

Note: The GTF files in the UCSC download server were created using the -utr flag. This adds the 5' and 3' utrs to the 9th field:

./genePredToGtf -utr hg38 refGene refGene.gtf

Bed format gene tracks (convert bed > genePred > GTF)

Some gene tracks are in a bed format in the database, perhaps with extra columns past the standard bed format. In this case, extract the standard bed columns, convert it to a genePred and then to a gtf. For example wgRna:

mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -N
-e "select chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd from wgRna;" hg19
| bedToGenePred stdin stdout | genePredToGtf file wgRna.gtf

Note that in the above methods, it was necessary to cut columns 1 - 10 to remove the extra trailing columns. With the method detailed here, this cut is not necessary in the case of using the database table since the command can determine from the table structure which columns to use.

Get a genePred file from UCSC MySQL public databases, then convert to GTF

Information about MySQl - http://genome.ucsc.edu/goldenPath/help/mysql.html

MySQL query example to get a genePred file:

$ mysql --host=genome-mysql.soe.ucsc.edu --user=genome -Ne "select a.name, a.chrom, a.strand, a.txStart, a.txEnd,
a.cdsStart, a.cdsEnd, a.exonCount, a.exonStarts, a.exonEnds, 0 as score, b.geneSymbol from knownGene a join
kgXref b on a.name=b.kgID" hg19 > hg19.genePred

Next, using the genePredToGtf utility:

genePredToGtf file hg38.genePred hg38.knownGene.gtf

genePred output will look like this:

uc001aaa.3 chr1 + 11873 14409 11873 11873 3 11873,12612,13220, 12227,12721,14409, 0 DDX11L1 uc010nxr.1 chr1 + 11873 14409 11873 11873 3 11873,12645,13220, 12227,12697,14409, 0 DDX11L1 uc010nxq.1 chr1 + 11873 14409 12189 13639 3 11873,12594,13402, 12227,12721,14409, 0 DDX11L1

Result:

chr1 hg19.genePred transcript 11874 14409 . + . gene_id "DDX11L1"; transcript_id "uc001aaa.3"; gene_name "DDX11L1"; chr1 hg19.genePred exon 11874 12227 . + . gene_id "DDX11L1"; transcript_id "uc001aaa.3"; exon_number "1"; exon_id "uc001aaa.3.1"; gene_name "DDX11L1"; chr1 hg19.genePred exon 12613 12721 . + . gene_id "DDX11L1"; transcript_id "uc001aaa.3"; exon_number "2"; exon_id "uc001aaa.3.2"; gene_name "DDX11L1"; chr1 hg19.genePred exon 13221 14409 . + . gene_id "DDX11L1"; transcript_id "uc001aaa.3"; exon_number "3"; exon_id "uc001aaa.3.3"; gene_name "DDX11L1";

The opposite direction, GTF to GenePred

There is a utility for this as well: gtfToGenePred. Here are some examples of using this utility:

$ wget ftp://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/MANE.GRCh38.v0.5.select_ensembl_genomic.gtf.gz $ gunzip MANE.GRCh38.v0.5.select_ensembl_genomic.gtf.gz $ head -n1 MANE.GRCh38.v0.5.select_ensembl_genomic.gtf chr1 ensembl_havana gene 944203 959309 . - . gene_id "ENSG00000188976.11"; gene_type "protein_coding"; gene_name "NOC2L";

BASIC USAGE

$ gtfToGenePred MANE.GRCh38.v0.5.select_ensembl_genomic.gtf MANE.GRCh38.v0.5.select_ensembl_genomic.genePred $ head -1 MANE.GRCh38.v0.5.select_ensembl_genomic.genePred ENST00000327044.7 chr1 - 944202 959256 944693 959240 19 944202,945056,945517,946172,946401,948130,948489,951126,951999,952411,953174,953781,954003,955922,956094,956893,957098,958928,959214, 944800,945146,945653,946286,946545,948232,948603,951238,952139,952600,953288,953892,954082,956013,956215,957025,957273,959081,959256,

EXTENDED USAGE

$ gtfToGenePred -genePredExt MANE.GRCh38.v0.5.select_ensembl_genomic.gtf MANE.GRCh38.v0.5.select_ensembl_genomic.genePredExt $ head -1 MANE.GRCh38.v0.5.select_ensembl_genomic.genePredExt ENST00000327044.7 chr1 - 944202 959256 944693 959240 19 944202,945056,945517,946172,946401,948130,948489,951126,951999,952411,953174,953781,954003,955922,956094,956893,957098,958928,959214, 944800,945146,945653,946286,946545,948232,948603,951238,952139,952600,953288,953892,954082,956013,956215,957025,957273,959081,959256, ENSG00000188976.11 cmpl cmpl 1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0,

For a full list of options available to gtfToGenePred, run the program with no args:

gtfToGenePred - convert a GTF file to a genePred usage: gtfToGenePred gtf genePred

options: -genePredExt - create a extended genePred, including frame information and gene name -allErrors - skip groups with errors rather than aborting. Useful for getting infomation about as many errors as possible. -ignoreGroupsWithoutExons - skip groups contain no exons rather than generate an error. -infoOut=file - write a file with information on each transcript -sourcePrefix=pre - only process entries where the source name has the specified prefix. May be repeated. -impliedStopAfterCds - implied stop codon in after CDS -simple - just check column validity, not hierarchy, resulting genePred may be damaged -geneNameAsName2 - if specified, use gene_name for the name2 field instead of gene_id. -includeVersion - it gene_version and/or transcript_version attributes exist, include the version in the corresponding identifiers.

Mailing List Resources about GTF

Please also try searching our mailing list for previous answers that may be of interest.

Scripting examples

Scripting to add IDs and other fields into the header of an .fa sequence file

Link to an archived help forum topic

Perl script to find and replace the "gene ID" with the Ensembl ID, which is named "transcript_id."

Example output prior to using the script below (in the next step). The output below is example output from the command genePredToGtf hg38 wgEncodeGencodeCompV24 hg38FileTest.gtf

chr1 wgEncodeGencodeCompV24 transcript 17369 17436 . - . gene_id "MIR6859-1"; transcript_id "ENST00000619216.1"; gene_name "MIR6859-1"; chr1 wgEncodeGencodeCompV24 exon 17369 17436 . - . gene_id "MIR6859-1"; transcript_id "ENST00000619216.1"; exon_number "1"; exon_id "ENST00000619216.1.1"; gene_name "MIR6859-1"; chr1 wgEncodeGencodeCompV24 transcript 29554 31097 . + . gene_id "RP11-34P13.3"; transcript_id "ENST00000473358.1"; gene_name "RP11-34P13.3"; chr1 wgEncodeGencodeCompV24 exon 29554 30039 . + . gene_id "RP11-34P13.3"; transcript_id "ENST00000473358.1"; exon_number "1"; exon_id "ENST00000473358.1.1"; gene_name "RP11-34P13.3"; chr1 wgEncodeGencodeCompV24 exon 30564 30667 . + . gene_id "RP11-34P13.3"; transcript_id "ENST00000473358.1"; exon_number "2"; exon_id "ENST00000473358.1.2"; gene_name "RP11-34P13.3";

Example output after running this perl script:

perl -wpe 's/gene_id "[^"]+"; transcript_id "([^"]+)"/gene_id "$1"; transcript_id "$1"/;' genePredToGtf.output

chr1 wgEncodeGencodeCompV24 transcript 17369 17436 . - . gene_id "ENST00000619216.1"; transcript_id "ENST00000619216.1"; gene_name "MIR6859-1"; chr1 wgEncodeGencodeCompV24 exon 17369 17436 . - . gene_id "ENST00000619216.1"; transcript_id "ENST00000619216.1"; exon_number "1"; exon_id "ENST00000619216.1.1"; gene_name "MIR6859-1"; chr1 wgEncodeGencodeCompV24 transcript 29554 31097 . + . gene_id "ENST00000473358.1"; transcript_id "ENST00000473358.1"; gene_name "RP11-34P13.3"; chr1 wgEncodeGencodeCompV24 exon 29554 30039 . + . gene_id "ENST00000473358.1"; transcript_id "ENST00000473358.1"; exon_number "1"; exon_id "ENST00000473358.1.1"; gene_name "RP11-34P13.3"; chr1 wgEncodeGencodeCompV24 exon 30564 30667 . + . gene_id "ENST00000473358.1"; transcript_id "ENST00000473358.1"; exon_number "2"; exon_id "ENST00000473358.1.2"; gene_name "RP11-34P13.3";