Jste zde

Analysis of high-throughput sequencing data

Termín: 
Čt, 27.11.2014 9:30 - Pá, 28.11.2014 16:00
Místo: 
VŠB - Technical University Ostrava, IT4Innovations building, room 450
Lektor: 
Paolo Ribeca (The Pirbright Institute, UK and Centro Nacional de Análisis Genómico, Spain)
Úroveň: 
basic
Jazyk: 
English

Annotation

High-throughput sequencing has revolutionized the way we understand biology. With state-of-the-art technologies one can nowadays re-sequence a human genome for less than 1,000$. However, key technical problems are still present. First, with current technologies one cannot sequence a long DNA molecule as a whole, but rather only read it out as many relatively short chunks; as a result, data analysis becomes complicated. Second, the convoluted interaction between biology, experimental protocols and sequencing is sometimes very hard to disentangle, requiring precise experimental designs. Third, the sheer amount of data forces people to design and use novel tools whose algorithmic behaviour is sometimes hard to grasp. In summary, the bioinformatics interpretation of the data remains complicated, computational expensive, and full of technical pitfalls that are sometimes not apparent at first sight.

Purpose of the course (benefits for the attendees)

This course will provide a basic introduction about how to correctly analyze high-throughput sequencing data. Several biological applications, experimental setups and sequencing protocols will be considered. A few hands-on sessions will be an essential part of the course.

About the tutor

Dr. Paolo Ribeca started working on the development of algorithms for the analysis of high-throughput sequencing data in 2008. He is the main architect of the GEM suite of bioinformatics programs (http://gemlibrary.sourceforge.net).

Schedule

Thursday,  November 27,  2014
09:30-10:00registration
10:00-11:30Basics of high-throughput sequencing
11:30-13:00time for lunch
13:00-14:30Alignment (basics; mapping)
14:30-15:00coffee break
15:00-16:30DNA-seq mapping hands-on
16:30-17:00coffee break
17:00-18:00Mapping, revisited (algorithms; protocols)

 

Friday,  November 28,  2014
09:00-10:30RNA-seq mapping hands-on
10:30-11:00coffee break
11:00-12:45Downstream analysis. Differential quantification
12:45-14:00time for lunch
14:00-15:30Basics of assembly

Prerequisities

Basic knowledge about Unix (Linux) operating system;  a laptop to follow actively the demonstrations on Anselm

Registration

Obligatory registration - registration form here; deadline 7 days before the event or exhausted course capacity.

Fees

The event is provided free of charge for the participants.

Capacity

20 attendees

Practicalities

  • See a special page on transport (in Czech) how to get to the campus of  VŠB - Technical University Ostrava and to the new IT4Innovations building.
  • Anselm training accounts will be distributed at the registration.
  • Anselm cluster documentation is available at http://support.it4i.cz/docs.
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