Hello Neeraja,
Thank you for your question about obtaining GTF output from the UCSC Table Browser. The GTF output options for the UCSC Table Browser are quite limited, and it does not have the ability to create GTF output as you request. We suggest that instead you use our command-line tool genePredToGtf, which generates GTF files with appropriate transcript IDs and gene symbols.
More information on using genePredToGtf is available on our wiki at http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format. You can find precompiled versions of the genePredToGtf program at http://hgdownload.soe.ucsc.edu/admin/exe/. If your computer architecture is not among those listed in that directory, you can also download the source code file userApps.src.tgz and compile the program yourself. To run the program on the hg38 refGene table, you will need to use the command
genePredToGtf hg38 refGene refGene.gtf
If you are unable to run the genePredToGtf tool, then you may be able to use the online text manipulation tools at Galaxy (https://usegalaxy.org) to edit the original GTF output from the UCSC Table Browser. Here is a mailing list question that discusses adding gene symbols with Galaxy: https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/T5UN1mt79Tc/discussion.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
--