Summary and Schedule
This is a new lesson built with The Carpentries Workbench.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction to genome browsers |
What are genome browsers and why are they useful? How was the human reference genome constructed? |
| Duration: 00h 20m | 2. Data used in this workshop | What data are we using in this workshop? |
| Duration: 00h 30m | 3. UCSC Genome Browser: Setup | How do we navigate the web interface of the UCSC Genome Browser? |
| Duration: 01h 00m | 4. UCSC Genome Browser: Understanding gene models | How do we interpret gene models represented in the UCSC genome browser? |
| Duration: 01h 40m | 5. UCSC Genome Browser: BLAT tool | What is the BLAT tool and how do we use it? |
| Duration: 02h 10m | 6. UCSC Genome Browser: Gene expression data | How can we explore gene expression data in the UCSC genome browser? |
| Duration: 02h 50m | 7. IGV | How do you use IGV? |
| Duration: 03h 50m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Workshop overview
This workshop will introduce you to the genome browser format and illustrate how some freely available genome browsers can be used to interrogate a variety of data types, such as gene expression, genomic variation, methylation and many more.
Learning objectives
At the end of this introductory workshop, you will:
- Understand the how some types of genomic and expression data are represented in genome browsers
- Understand gene models and identify differences between transcript variants
- Determine the tissue/cell type expression profiles of a gene of interest in mouse and human expression data
- Know some basic files types used in genome browsers and upload and view local BAM files.
- Use the BLAT tool to locate genomic regions with similarity to a sequence of interest
- Create custom interactive views with multiple datatypes to share with colleagues and generate images for publications
By focusing on gene expression, this hands on tutorial will provide beginners with an introduction to both the UCSC Genome Browser and IGV (Integrative Genomics Viewer).
Tools and public datasets will be used to illustrate how the expression of transcript variants can be investigated in different tissues and cell types using public data.
The data and genes used in this workshop are taken from the neuroscience field, however the analysis approaches and tools illustrated can be applied to many research areas.
Public data viewed within the UCSC genome browser in this workshop includes human RNAseq data from GTEX and mouse cell type RNAseq data from Tabula Muris, while a subset of Single cell RNAseq data from the Allen Brain Atlas Celltax study will also be downloaded from SRA and visualised in IGV.
Timing
The anticipated workshop duration when delivered to a group of participants is 4 hours. Note that not all the exercises are expected to be completed during the workshop.
Skill level
This workshop is designed for participants with no previous experience using genome browsers and no programming experience.
Requirements and preparation
DEVICE
Attendees are required to provide their own laptop computers
REQUIRED SOFTWARE
Prior to the workshop:
- Download and install IGV (free)
- Ensure that Chrome or FireFox are installed and up to date
- Create a user account in the UCSC Genome Browser
This workshop will be run using the above freely available web interfaces and free software with graphical user interfaces.
REQUIRED DATA
No additional data needs to be downloaded prior to this workshop. Required data will be downloaded as part of the tutorial exercises.