Genomics for working with pathogens (Brazil)
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Date:
Monday 26 - Thursday 29 May 2014Venue:
Centro de Pesquisas René Rachou – Fundação Oswaldo Cruz - entro de Pesquisas René Rachou – Fundação Oswaldo Cruz, Av. Augusto de Lima, 1715, Belo Horizonte, MG, 30190-002, United KingdomApplication deadline:
Monday 12 May 2014Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
R$ 300,00Registration closed
Course Overview
This course will provide delegates with hands-on training in annotation genomes and accessing genomic information via the Ensembl Genomes browser, for those working in the area of pathogen genomes. An overview of high throughput sequencing workflows and analysis (mainly using RNA-seq) will be presented, including introductions to the use of R and Bioconductor.
Audience
This course is aimed at PhD students and post-doctoral researchers who are working with pathogen genomes and wish to gain hands-on training in RNA-seq analysis and genome annotation. Familiarity with the technology and biological use cases of high throughput sequencing is required, and some experience with R/Bioconductor would be beneficial.
Learning outcomes
After this course you will be able to:
- Search, query and retrieve genomic data from public repositories
- Use bioinformatics tools to estimate gene expression levels
- Discuss a variety of bioinformatic techniques for genome annotation
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 26 May 2014 |
||
| 09:00 | Course introduction and overview | Guilherme Corrêa de Oliveira |
| 09:30 | Overview of sequence data for genome annotation | Gabriel da Rocha Fernandes |
| 10:30 | Tea/coffee break | |
| 11:00 | Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R | Benilton Carvalho |
| 12:00 | Lunch | |
| 13:30 | Practical: Introduction to Unix | Gabriel da Rocha Fernandes |
| 14:45 | Practical: Introduction to R/Bioconductor | Benilton Carvalho |
| 15:30 | Tea/coffee break | |
| 16:00 | Q&A Session | |
| 17:15 | End | |
| Day 2 - Tuesday 27 May 2014 |
||
| 09:00 | Lecture: Estimating expression over genes and exons | Gabriel da Rocha Fernandes |
| 10:00 | Tea/coffee break | |
| 10:30 | Practical: Estimating expression over genes and exons | Gabriel da Rocha Fernandes |
| 12:30 | Lunch | |
| 14:00 | Lecture: Statistical concepts and methodologies for data analysis | Benilton Carvalho |
| 16:00 | Tea/coffee break | |
| 16:30 | Practical: Statistical concepts and methodologies for data analysis | Benilton Carvalho |
| 17:30 | Q&A session | |
| 18:00 | End | |
| Day 3 - Wednesday 28 May 2014 |
||
| 09:00 | Genome alignments: Repeat masking, EST alignments & short read mapping (Introduction and hands-on) | Uma Maheswari |
| 10:30 | Tea/coffee break | |
| 11:00 | Genome annotation: ab initio gene prediction, using expression data (EST and RNASeq), MAKER genome annotation (Introduction and hands-on) | Uma Maheswari |
| 12:00 | Lunch | |
| 13:30 | Browsing Ensembl Protists (Introduction) | Denise Carvalho-Silva |
| 14:00 | Browser walkthrough | Denise Carvalho-Silva |
| 15:30 | Tea/coffee break | |
| 16:00 | Browser exercises | |
| 16:30 | Quick data access with BioMart (Introduction) | Denise Carvalho-Silva |
| 17:00 | BioMart exercises | Denise Carvalho-Silva |
| 18:30 | End | |
| Day 4 - Thursday 29 May 2014 |
||
| 09:00 | Genome annotation (cont.) | Uma Maheswari |
| 10:30 | Tea/coffee break | |
| 11:00 | SNP calling | Uma Maheswari |
| 12:00 | Lunch | |
| 13:30 | Ensembl Protists browser: variation and VEP | Denise Carvalho-Silva |
| 14:30 | Variation exercises | Denise Carvalho-Silva |
| 15:30 | Tea/coffee break | |
| 16:00 | Comparative Genomics (Introduction and Hands-on) | Denise Carvalho-Silva |
| 17:00 | Ensembl Protists Wrap up, feedback survey | Denise Carvalho-Silva |
| 18:00 | Close of course | Guilherme Corrêa de Oliveira |
In association with
How to apply
Registration is now closed
Application deadline
12 May 2014
Organisers
Guilherme Oliveira - Instituto Tecnológico Vale - ITV - Vale Technological Institute
Sarah Morgan - EMBL-EBI, UK
Trainers
Guilherme Oliveira - Instituto Tecnológico Vale - ITV - Vale Technological Institute
Gabriel da Rocha Fernandes - Universidada Catolica de Brasilia
Benilton Carvalho - State University of Campinas - UNICAMP
Uma Maheswari - EMBL-EBI, UK
Denise Scholtens - Northwestern University Feinberg School of Medicine, USA