Introduction
^^^^^^^^^^^^

This directory contains GTF files for the main gene transcript sets where available. They are
sourced from the following gene model tables: ncbiRefSeq, refGene, ensGene, knownGene

Not all files are available for every assembly. For more information on the source tables
see the respective data track description page in the assembly. For example:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refGene

Information on the different gene models can also be found in our genes FAQ:
    https://genome.ucsc.edu/FAQ/FAQgenes.html

Generation
^^^^^^^^^^

The files are created using the genePredToGtf utility with the additional -utr flag. Utilities
can be found in the following directory:
    http://hgdownload.soe.ucsc.edu/admin/exe/

An example command is as follows:
    genePredToGtf -utr hg38 ncbiRefSeq hg38.ncbiRefSeq.gtf

Additional Resources
^^^^^^^^^^^^^^^^^^^^

Information on GTF format and how it is related to GFF format:
    https://genome.ucsc.edu/FAQ/FAQformat.html#format4

Information about the different gene models available in the Genome Browser:
    https://genome.ucsc.edu/FAQ/FAQgenes.html

More information on how the files were generated:
    https://genome.ucsc.edu/FAQ/FAQdownloads.html#download37

      Name                                             Last modified      Size  Description
      Parent Directory                                                      -   
      md5sum.txt                                       2024-03-04 15:38  162   
      mm39.ncbiRefSeq.gtf.gz                           2024-02-14 08:28   29M  
      mm39.knownGene.gtf.gz                            2023-08-29 15:16   20M  
      refGene.gtf.gz                                   2020-09-10 12:36   10M