CABANA Workshop: Introduction to Next-generation Sequencing

Date:

 Monday 18 Wednesday 20 March 2019

Venue: 

LANGEBIO, Cinvestav - LANGEBIO, Cinvestav, Libramiento Norte Carretera Leon Km 9.6, Irapuato,  GUA,  36821, Mexico

Application opens: 

Friday 14 December 2018

Application deadline: 

Sunday 03 February 2019

Participation: 

Open application with selection

Contact: 

Marina Pujol

Registration fee: 

$700 MXN

Registration closed

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Course Overview

This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data.

Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets and there will not be scope to analyse personal data. The course content makes use of data derived mainly from eukaryotic non-model organisms in a biodiversity context.
 

Audience

This course is suitable for postgraduate wet-lab researchers at any career stage within Latin America who are working with and/or generating their own transcriptomic datasets.
 
Participants will require a basic knowledge of the Unix command line and the R statistical package. We recommend these free tutorials:

 Participants without basic knowledge of these resources will have difficulty in completing the practical sessions. We strongly recommend that you make every effort to access these materials and other training available online or within your host institute to best prepare you for the course.
 
A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.
 

Modules

  • introduction-ensemblensembl-genomes

Learning outcomes

After this course you should be able to:

  • Describe NGS and its applications in biological research
  • Perform read alignments
  • Assemble transcriptomes
  • Perform differential gene expression analysis and visualize results in R and ggplot2 
  • View and explore data using Ensembl genome browser

Programme

Day 1 – Monday 18 Mar 2019
09:00-09:20 Welcome  
09:20-10:30 Introduction to high-throughput (NGS) sequencing technologies and applications (lecture) Selene Fernandez
10:30-11:00 Coffee Break
11:00-13:00 Introduction to the fastq format and quality control of NGS data (lecture + prac) Selene Fernandez
13:00-14:00 Lunch
14:00-15:00 Read alignment (lecture) Selene Fernandez
15:00-15:20 Short Break  
15:20-17:00 Read alignment (practical)     Selene Fernandez
17:00-17:30 Wrap-up Selene Fernandez
Day 2 – Tuesday 19 March 2019
09:00-10:30 Genome guided transcriptome assembly (lecture + practical) Selene Fernandez
10:30-11:00 Coffee Break
11:00-13:00 Genome guided transcriptome assembly (practical continued) Selene Fernandez
13:00-14:00 Lunch
14:00-16:00 Differential gene expression analysis (lecture + practical) Selene Fernandez
16:00-17:00 Keynote lecture Peter Stadler
17:00-17:30 Wrap-up Selene Fernandez
18:00-20:00 Social event (Faculty club)  
Day 3 – Wednesday 20 March 2019
09:00-10:30 Ensembl Genome browser (webinar) Erin Haskell
10:30-11:00 Coffee Break
11:00-12:00 Ensembl Genome browser (webinar)     Erin Haskell
12:00-13:00 Exploring differential expression results in R (ggplot2 practical) Selene Fernandez
13:00-14:00 Lunch
14:00-15:00 Exploring differential expression results in R (ggplot2 practical) Selene Fernandez
15:00-15:20 Short break  
15:20-17:00 Exploring differential expression results in R (ggplot2 practical) Selene Fernandez
17:00-17:30 Course close and feedback Selene Fernandez