Reference Code backup Executable files
Convert genePred table or file to gtf.
genePredToGtf database genePredTable output.gtf
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.
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 -f 2- in.gp | genePredToGtf file stdin out.gp
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
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