Getting Help with the UCSC Genome Browser

Teaching with the Genome Browser

NEW: See our tutorials page for new tutorials covering common Genome Browser functionalities.

Contact us to host a Genome Browser Workshop! Map

Now taking reservations for face-to-face workshops in the US and abroad !

Do you suspect that there is a lot more to the Genome Browser than you have been using? Timeslots are available to host a Genome Browser workshop at your institution, tailored to your audience's level of expertise.

For more information or to submit a request to host a workshop, please contact us.

Online training and tutorials

Our video tutorials address some common questions we've gathered from our mailing list. Along the way we try to show you interesting features of the Browser you may not have found on your own.

Visit our YouTube channel or use the links below.

Video tutorials

Browser Basics, Part One: Getting around in the Browser. [transcript]

Browser Basics, Part Two: Configuring the Browser. [transcript]

Browser Basics, Part Three: Configuration + DNA navigation. [transcript]

Making Links, Part One: Understanding the URL. [transcript]

Making Links, Part Two: Jump into genes. [transcript]

Making Links, Part Three: Composites, custom tracks, spreadsheets. [transcript]

Coronavirus Basics: Coronavirus Browser SARS-CoV-2. [transcript]

Saving and sharing sessions in the Browser. [transcript]

Controlling visibility of data tracks in the Browser. [transcript]

Using the isPCR tool (isPCR) in the UCSC Genome Browser. [transcript]

dbSNP resources in the UCSC Genome Browser database. [transcript]

Using the UCSC Genome Browser Data Integrator. [transcript]

Video tutorials

Finding a list of genes in a region. [transcript]

Finding exon numbers. [transcript]

Finding all SNPs in a gene. [transcript]

Finding SNPs upstream from a gene. [transcript]

Find which tables belong to a data track. [transcript]

Identifying codon numbers in a gene. [transcript]

Obtaining exon coordinates and sequences. [transcript]

Multi-Region View: Exon-only display mode. [transcript]

Multi-Region View: Alternate haplotypes. [transcript]

Multi-Region View: Discontinuous regions. [transcript]

How-to: Genome Browser in the Cloud.

How-to: Genome Browser Gateway.

Other content produced at UCSC

See a collection of interesting Browser views in our Session Gallery

Nature: Guide to the UCSC Genome Browser

Fishing for genes in the UCSC Browser (pdf)

The UCSC genome browser and associated tools

UCSC genome browser tutorial

Step-by-step tutorial presented at ASHG 2009 annual meeting - basic browser navigation and functionality in the context of interpreting clinical genetics reports.

Step-by-step tutorial presented at ABRF 2010 annual meeting - how to convert files and display high-throughput sequencing results.

Step-by-step tutorial presented at ASHG 2014 annual meeting - includes Custom Tracks and Table Browser queries with and without filters.

External resources

Teaching bioinformatics and neuroinformatics by using free web-based tools - student-level tutorial that demonstrates the combined use of several major bioinformatic tools (including the UCSC Genome Browser) in answering a series of related research questions

User's guides for tools in the Genome Browser

Genome Browser tutorials

Genome Browser

Custom Tracks

Track Hubs

Sessions

Table Browser

Data Integrator

Variant Annotation Integrator

Gene and Pathways Interactions

Genome Graphs

Gene Sorter

Genome Browser in a Box (GBiB)

Genome Browser in the Cloud (GBiC)

GBiC Docker

Contact and mailing list information

Genome Browser contact information

Genome Browser mailing list (searchable interactive discussion forum)

Genome Browser FAQs

Mirroring and source code

Genome Browser mirror sites

Obtaining the Genome Browser source code

Associated publications and announcements

Selected Genome Browser publications
Genome Browser news archives

Help pages for selected parts of the Genome Browser

Querying the Genome Browser

Configuring graph-based tracks

Configuring Subtracks

Configuring BAM tracks

Configuring VCF tracks

Configuring Hi-C heatmaps

Base Coloring for Alignment Tracks

Codon Coloring for Gene Tracks

Codon and Base Coloring for Alignments

Track Search

File Search

MySQL access

Multi-Region Display

LiftOver tracks

IUPAC codes

Asia and Euro Mirror

Overview: Browser Mirror Installation

Manual: Browser Mirror Installation

Track Hub Database Definitions

Public Hub Guidelines

Assembly Hub Wiki

TwoBit Sequence Archives

Building Trix Indices

Gene Haplotype Alleles

Motif Display Help Page

Alignment Insertion/Deletion Display

Data Formats Page