Video Guide for New Users

UCSC Genome Browser Basics

UCSC Genome Browser Basics. Part 1: Getting around in the Browser

• Would help to look at the Gateway page (Home page). The “Our story” paragraph was helpful.

https://genome.ucsc.edu/cgi-bin/hgGateway

• The Genome Browser User Guide has more information on the Genome Browser gateway.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GetStarted

• This also is a helpful video on the Genome Browser gateway.

https://www.youtube.com/watch?v=5zc9sqd4SD4&list=UUQnUJepyNOw0p8s2otX4RYQ&index=17

• The video does a good job of introducing the UCSC Genome browser graphic and a good quick description of data tracks.

• The Genome Browser User Guide has more information on Annotation track descriptions.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#IndivTracks

• The track search help page has information on searching tracks

https://genome.ucsc.edu/goldenPath/help/trackSearch.html

• The video also goes over some helpful tricks:, Switching the orientation of the DNA on the screen and navigating by cytoband.

• The Querying the Genome Browser help page has some good examples on how to query the Genome Browser.

https://genome.ucsc.edu/goldenPath/help/query.html

• Display single, canonical isoform only clip was a good example on why a new user would want to use the configuration options.

• The Genome Browser User Guide has more information on configuring the Genome Browser display.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning

Controlling the visibility of data tracks on the UCSC Genome Browser

• This video does a good job mentioning and describing BED3 format.

• The Data Formats Page has more information about BED format:

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

• The mouseover feature could be useful for a user.

• The following video has another example of mouseover and finding tablename by table schema.

https://youtu.be/RQZ4EeYS6Zk?t=165

• The super tracks and wiggle tracks examples with different track displays made it sink in why the track displays are helpful.

• The Configuring Subtracks help page has more about controlling composites

http://genome.ucsc.edu/goldenPath/help/multiView.html

• The Configuring graph-based tracks help page has more information about controlling wiggle tracks:

http://genome.ucsc.edu/goldenPath/help/hgWiggleTrackHelp.html

UCSC Genome Browser Basics, Part 2: Configuring the Browser

• The Next / Previous Item arrows clip was really a good demo.

• The Genome Browser User Guide has more information on Next/previous item navigation in the“Enabling item and exon navigation” section.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK_CONFIG

Finding exon numbers

Great explanation of the alternate colors in the exon. The demo on how to navigate by arrows on the browser graphic was excellent. A new user would benefit on how the arrows on the browser graphic feature may differ depending on the zoom.

• The Genome Browser User Guide has more information on zoom, display adjusting, highlighting, and exon navigation.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#NAV

UCSC Genome Browser Basics. Part 3: Configuration + DNA navigation

• The Run BLAT with mismatches clip was a really good demo.

• The Genome Browser User Guide has more information on Blat.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

• The Short Match track demo was great. I did not know that Short Match would find the sequence in minus strand as well.

UCSC Genome Browser Sessions

Saving and Sharing Sessions on the UCSC Genome Browser

• The Session User Guide has more information on sessions.

https://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html#Introduction

UCSC Genome Browser Table Browser

Finding a list of genes in a region

• The Table Browser demo was great.

• The Table Browser User guide has more information on simple data queries using the Table Browser.

https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#GettingStarted

• The knownCanonical table demo was great. A new user can benefit from knowing the different options in the primary table such as the knownCanonical table.

• The FAQ genes page has more information on knownCanonical.

https://genome.ucsc.edu/FAQ/FAQgenes.html#singledownload

SNPs

Finding SNPs upstream from a gene

The Intersect upstream regions with the SNP track demo was a great example of how to use the intersection feature.

• The Table Browser User Guide has more information on intersecting data from multiple tables.

https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection

dbSNP resources in the UCSC Genome Browser database

• This was a great video. The comparison of SNPs in tracks was helpful for a new user and for someone that has not worked with SNPs.
• The demo on two ways to navigate between genomes was very helpful for a new user.

• The Genome Browser User Guide has more information on converting data between assemblies.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert

• Here is a great demo on confirming codon numbers with OMIM AV SNPs and UniProt Variants. This shows new users the rich resources that the genome browser can provide through the confirmation of mutations of different gene tracks.

https://youtu.be/bLnfD799AZw?t=345

Exons

Obtaining exon coordinates and sequences

• The zoom out drag method of the ideogram demo is a good feature and not mentioned in the user guides.
• The description of the demo’s BED output was great.
• Great add custom tracks demo.

UCSC Genome Browser Multi-Region View

Multi-Region View: Exon-only display mode

• The RNA-seq data in exon-only mode demo was a great example on how to enhance the browser display and why users would want to do exon only mode.

• The Multi-Region Display Help page has more information on exon-only mode and some good examples.

https://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html#ExonOnly

Multi-Region View: Alternate haplotypes

• Great demo on the Blat the alt ends and going over the BLAT search results.

• The Multi-Region Display Help page has more information on Custom regions mode haplotype mode.

https://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html#Haplotype

Multi-Region View: Discontinuous regions

• The Get help demo on how to find the Multi region modes: “custom region” is helpful for a new user.

• The Multi-Region Display Help page has more information on Custom regions mode.

https://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html#CustomRegions

• The Genome Browser FAQ page

https://genome.ucsc.edu/FAQ/

UCSC Genome Browser Data Integrator

Using the UCSC Genome Browser Data Integrator

• The demo was great and easy to follow. For new users that use excel to analyze data, the Load data into spreadsheet demo would be useful.

• The Data Integrator User's Guide has more information on the Data integrator.

https://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html#Intro

UCSC Genome Browser isPCR

Using the isPCR tool (isPCR) in the UCSC Genome Browser

• The demo was great and easy to follow. Great example on using primers to predict amplicon size from genome assembly and RNA template. Mentioning that the UCSC genes are the in-silico equivalent of having spliced mRNA as a template was helpful.

UCSC Genome Browser Coronavirus Browser

Coronavirus Basics: Coronavirus Browser SARS-CoV-2

• The video shows the resourcefulness and power of the UCSC Genome Browser. The BLAST Search Results for mismatch demo was excellent. The different ways of seeing the mismatches helps a new user.

• The COVID-19 Pandemic Resources at UCSC page has more information on the Coronavirus Browser SARS-CoV-2

https://genome.ucsc.edu/covid19.html

Making Links

Making Links, Part One: Understanding the URL

• Explanation of why not to share a direct link was helpful. The toolbar link example was great. This shows how the toolbar link can be a utility to a new user.

• The FAQ Linking to the Genome Browser page has more information on creating a shareable URL to view specific tracks

https://genome.ucsc.edu/FAQ/FAQlink.html#link1

Making Links, Part Two: Jump into genes

• The cart demo was excellent. A new user can experiment with the variables and get more of an understanding on what they do.

Making Links, Part Three: Composites, custom tracks, spreadsheets

• The explanation on visibility comes on at the default setting for composite tracks was helpful.

• The Quick Start Guide to Organizing Track Hubs into Groupings help page has more information on understanding composite tracks.

https://genome.ucsc.edu/goldenpath/help/hubQuickStartGroups.html#composite

• The remote hosting demo was helpful.

• The Using UCSC Genome Browser Track Hubs help page has more information on data hosting.

https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting

Genome Browser in the Cloud

How-to: Genome Browser in the Cloud

• Good introduction to Genome Browser in the Cloud (GBiC). The step by step on the command line is helpful for a new user.

• The Genome Browser in the Cloud User's Guide has more information on GBiC.

https://genome.ucsc.edu/goldenPath/help/gbic.html#what-is-genome-browser-in-the-cloud