CABANA Workshop: Advanced RNAseq and Network Analysis in Genomics

Date:

 Wednesday 6 Saturday 9 November 2019

Venue: 

Instituto de Biología Agrícola de Mendoza / Institute of Agricultural biology (IBAM) - Almirante Brown 500, Chacras de Coria, M5528AHB,  Mendoza,  Mendoza, Argentina

Application opens: 

Wednesday 31 July 2019

Application deadline: 

Sunday 01 September 2019

Participation: 

Open application with selection

Contact: 

Derrin Crawte

Registration fee: 

$1500 ARS

Registration closed

Find other similar courses »

Course Overview

This course will provide training on RNAseq data production and interpretation. The course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. We will dedicate some time to analysing and constructing networks from expression data and using the Gene Ontology for gene set enrichment test. Finally, we will cover some aspects of Meta-metrics in networks (high-dimensional data).

 

Syllabus, Tools and Resources

During this course you will learn about: 

  • NGS: Introduction to RNAseq and Overview of Course
  • Mapping of Reads to reference & Expression estimation; Count data
  • Differential Expression
  • Ontology (properties) & Gene Ontology & GeneSet Enrichment test
  • Complex systems and systems biology
  • Biological Networks / Network basic concepts / Expression networks

Audience

This course is aimed at researchers from Masters-level upwards within Latin America who are working with and/or generating their own plant genomic and transcriptomic datasets. 

Prerequisites:
Some basic computational or previous bioinformatics experience is required for this workshop, particularly using the UNIX operating system (basic command line skills) and R.

You may find the resources below useful:

Important: All participants must bring a laptop for the course. We will use a virtual machine (VM) provided by instructors for the course practical sessions. All laptops must be of 64-bit architecture with any Operating System and have at least 60 GB free space.

Please also note: this course will be taught in Spanish, however the trainers are fluent in English and can offer language support where feasible.

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.
 

Learning outcomes

After this course you should be able to:

  • Describe and perform basic RNAseq data cleanup and processing
  • Analyze RNAseq data and its expression estimation
  • Conduct differential expression analysis
  • Conduct gene set enrichment analysis
  • Conduct network analysis in complex biology systems

Programme

Day 1: RNAseq data cleanup, processing and expression estimation
Day 2: Differential expression and gene set enrichment analysis
Day 3: Complex systems, systems biology and Network analysis
Day 4: Coexpression networks and meta-metrics in networks

Day 1 – Wednesday 6 November 2019
08:30-09:00 Arrival and registration  
09:00-10:00 NGS: Introduction to RNAseq and Overview of Course Maximo Rivarola
10:00-11:00 Dealing with raw data; Filtering and QC Maximo Rivarola / Sergio Gonzalez
11:00-11:30 Break
11:30-13:00 Mapping of Reads to reference & Expression estimation; Count data Maximo Rivarola
13:00-14:00 Lunch
14:00-15:30 Dealing with align data. QC and working with SAM/BAM files  & Expression estimation Maximo Rivarola / Sergio Gonzalez
15:30-16:00 Break
16:00-17:30 Expression estimation Maximo Rivarola
17:30 End of day 1  
Day 2 – Thursday 7 November 2019
09:00-11:00 Differential Expression Maximo Rivarola
11:00-11:30 Break
11:30-13:00 Ontology (properties), Gene Ontology & Gene Set Enrichment test Sergio Gonzalez
13:00-14:00 Lunch
14:00-15:30 Gene Set Enrichment test Maximo Rivarola / Sergio Gonzalez
15:30-16:00 Break
16:00-17:30 Gene Set Enrichment test (continued) Speaker Name / Group Name
17:30 End of day 2  
Day 3 – Friday 8 November 2019
09:00-10:00 Complex systems and systems biology Ariel Chernomoretz
10:00-11:00 Complex systems and systems biology Maximiliano Beckel / Andrés Rabinovich
11:00-11:30 Break
11:30-13:00 Biological Networks / Network basic concepts / Expression networks Ariel Chernomoretz
13:00-14:00 Lunch
14:00-15:30 Biological Networks / Network basic concepts Maximiliano Beckel / Andrés Rabinovich
15:30-16:00 Break
16:00-17:30 Biological Networks / Network basic concepts (continued) Maximiliano Beckel / Andrés Rabinovich
17:30 End of day 3  
Day 4 – Saturday 9 November 2019
09:00-10:00 Coexpression Networks (weighted networks) Ariel Chernomoretz
10:00-11:00 Coexpression Networks (weighted networks) Maximiliano Beckel / Andrés Rabinovich
11:00-11:30 Break
11:30-13:00 Meta-metrics in networks (high-dimension data) Ariel Chernomoretz
13:00-14:00 Lunch
14:00-15:30 Meta-metrics in networks (high-dimension data) Maximiliano Beckel / Andrés Rabinovich
15:30-16:00 Break
16:00-17:30 Coexpression Networks Ariel Chernomoretz
17:30-17:45 Course wrap-up and feedback Course organizers
17:45 End of course