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Informatics on High Throughput Sequencing Data

Workshop Details

Date: July 29-30, 2010
Location: Downtown Toronto, ON
Lead Faculty (2010): Asim Siddiqui, Michael Stromberg, Ryan Morin & Francis Ouellette
Registration Fee for Applications received before June 28, 2010: $500 + HST
Registration Fee for Applications received after June 28, 2010: $700 + HST
SOLD OUT

Target Audience
This workshop is geared to graduate students, post-doctoral fellows, clinical fellows and investigators involved in analyzing data from HT sequencing platforms.

Prerequisite: Your own laptop computer. If you do not access to a laptop, you may loan one from the CBW for a fee. Please contact course_info@bioinformatics.ca for more information.


Course Objectives
With the introduction of high-throughput sequencing platforms from Illumina, Roche and ABI, it is becoming feasible to consider sequencing approaches to address many research projects. However, knowing how to manage and interpret the large volume of sequence data resulting from such technologies is less clear. The CBW has developed a 2-day course covering the bioinformatics tools available for managing and interpreting high-throughput sequencing data.

Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to:

  • Assess sequence quality
  • Map sequence data onto a reference genome
  • Quantify sequence data
  • Integrate biological context with sequence information



Course Outline

Day 1
Module 1: Introduction to next generation sequencing (Faculty: Francis Ouellette)

  • Types of platforms
  • Common applications and issues

Break (30 minutes)

Module 2: File Types (Faculty: Asim Siddiqui)

  • Types of files from next generation sequencers
  • Working with files in R/Perl/Awk
  • QA/QC of raw data

Lunch

Module 3: RNA Seq (Faculty: Ryan Morin)

  • Alignment of RNA-seq data
  • Variant identification and annotation of variants
  • Expression and alternative expression (splicing) measurement

Break (30 minutes)

Laboratory - RNA Seq Analysis

Dinner

Open Lab

Day 2
Module 4: Genome variation - SNPs (Faculty: Michael Stromberg)

  • Single Nucleotide Polymorphism (SNP) Sequence Data
  • Structural Genome Variations/Chromosome rearrangements
  • Copy Number Variations (CNVs)

Break (30 minutes)

Laboratory - Genome Variation

Lunch

Lab - Genome Variation (continued)

Module 5: Data management (Faculty: Asim Siddiqui)

  • Data centre fundamentals: dealing with data, tips and tricks
  • Data standards

Break (30 minutes)

Module 6: Visualization (Faculty: Francis Ouellette)

Pre-Readings
http://www.ncbi.nlm.nih.gov/pubmed/18576944
http://www.ncbi.nlm.nih.gov/pubmed/18349386