Genomics Workshop at Avian Models Systems - CSHL, USA

Date:

  Tuesday 4 March 2014

Venue: 

Grace Auditorium, Cold Spring Harbor Laboratory - Grace Auditorium, Cold Spring Harbor Laboratory, New York, , NY,  NY 11724-2213, United States

Participation: 

Open application with selection

Contact: 

Holly Foster

Registration closed

Course Overview

We are pleased to announce a Cold Spring Harbor winter biotechnology conference on Avian Model Systems  which will begin on Wednesday evening, March 5 and end at noon on Saturday, March 8, 2014. The meeting will be preceeded by a 2-day Avian Genomics workshop run in collaboration with EMBL-EBI and WTSI, which will begin at 9:00 a.m. on Tuesday March 4 and end before dinner on Wednesday March 5, just prior to the start of the main meeting.

This workshop will provide an introduction to using public resources to study avian genomics, and to NGS sequence analysis.

Audience

This workshop is aimed at biologists who are interested in using avian genomes in their work.

Learning outcomes

After this workshop you will be able to:

  • Search, query and retrive data from public resources for avian genome data
  • Use bioinformatics tools to process and analyses NGS data

Programme

Time Topic Trainer
Day 1 - 4 March 2014
09:00-11:00 Browsing Avian Genomes with Ensembl (Lecture and Hands-on) Denise Carvalho-Silva 
11:00 - 11:30 Tea/coffee break  
11:30 - 12:30 Browsing Avian Genomes with Ensembl (Lecture and Hands-on) (+ Introduction to BioMart) Denise Carvalho-Silva
12:30 - 13:30 Lunch  
13:30 - 15:00 Browsing Avian Genomes with Ensembl (Lecture and Hands-on) (Going Deeper) Denise Carvalho-Silva
15:00 - 15:30 Tea/coffee break  
15:30 - 16:00 Lecture: Next generation sequencing overview  Myrto Kostadima/Remco Loos
16:00 - 17:00 Lecture & Practical: NGS quality control Myrto Kostadima/Remco Loos
19:00 - 20:30 Lecture & Practical: Sequence alignment Myrto Kostadima/Remco Loos
20:30 - 21:30 Lecture: Introduction to ChIP-seq Myrto Kostadima/Remco Loos
Day 2 - 5 March 2014
09:00 - 10:30 Practical: ChIP-seq - peak calling and annotation (with quick coffee break) Myrto Kostadima/Remco Loos
10:30 - 12:00   Practical: ChIP-seq - motif analysis Myrto Kostadima/Remco Loos
12:00 - 13:00 Lunch  
13:00 - 14:00 Lecture: Transcriptome assembly and differential expression analysis Myrto Kostadima/Remco Loos
14:00 - 15:30 Practical: Reference guided transcriptome assembly (with quick coffee break) Myrto Kostadima/Remco Loos
15:30 - 17:00  Practical: Differential expression analysis Myrto Kostadima/Remco Loos