Video Guide for New Users

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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 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

  • The Data Formats Page has more information about BED format:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1
  • The following video has another example of mouseover and finding tablename by table schema.
https://youtu.be/RQZ4EeYS6Zk?t=165
  • 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 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 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 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

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

  • 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

Obtaining exon coordinates and sequences


UCSC Genome Browser Multi-Region View

Multi-Region View: Exon-only display 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

  • 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


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 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 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