genePredToGtf

Reference Code backup Executable files

Convert genePred table or file to gtf.

Category

Genome Annotation

Usage

genePredToGtf database genePredTable output.gtf

Manual

This tool is part of UCSC Genome Browser's Utility Tools.

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 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

Examples

Dump GENCODE V26 (for the human genome assembly hg38), Basic Genes and Gene Predictions (wgEncodeGencodeBasicV26) from UCSC Table Browser and save the annotations to a file named utilityOutputBasic26.gtf

genePredToGtf hg38 wgEncodeGencodeBasicV26 utilityOutputBasic26.gtf

If you have downloaded a table (for example, the knownGene table for hg19) from UCSC, which will be in genePred format. You can then use this local file as input for the genePredToGtf conversion:

wget ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz  # download the table from UCSC
zcat knownGene.txt.gz | cut -f1-10 | genePredToGtf file stdin knownGene.gtf  # convert the table to gtf format

 

Share your experience or ask a question