Index of /goldenPath/hg38/bigZips/genes

	Name	Last modified	Size	Description
	Parent Directory		-
	md5sum.txt	2023-08-29 15:26	221
	hg38.refGene.gtf.gz	2020-01-10 09:33	23M
	hg38.ncbiRefSeq.gtf.gz	2023-11-22 10:02	42M
	hg38.knownGene.gtf.gz	2024-04-02 11:55	38M
	hg38.ensGene.gtf.gz	2020-01-10 09:33	27M
	README.txt	2023-11-01 13:20	2.1K
	README.html	2020-12-18 07:04	2.6K

Contents

Introduction

Generation

Additional Resources

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