You are here

Introduction to Genomic Analysis Workshop Series

Date:

Monday, June 5, 2017 to Wednesday, June 14, 2017

Speaker Info:

Phillip Richmond
PhD Student, Wasserman Lab, Centre for Molecular Medicine and Therapeutics
BC Children's Hospital, University of British Columbia

Description

Held over the course of seven days (June 5-9 and June 12-14), this workshop series will cover:

  • an introduction to linux how to use WestGrid / Compute Canada high performance computing resources
  • DNA sequencing analysis including variant calling and annotation
  • RNA-seq analysis pipelines for identifying differential expression

Within this workshop we will use cutting-edge open source software frequently used by researchers in the field.

Course Details:

  • 7 sessions, 1 mid-series 'exam'
  • Sessions will take place from June 5-9 and June 12-14
  • Sessions will be held from either 10am - 12pm Pacific or 9:30 - 11:30 am (see schedule for times)
  • Participants can attend in-person at the BC Children's Hospital (see schedule for locations) or online via videoconference

Schedule:

  • Monday, June 5 - Introduction to Linux I, Basic Command Line
    10am-12pm Pacific - Room #3113, BC Children's Hospital

  • Tuesday, June 6 - Introduction to Linux II, Interacting with the Queue
    10am-12pm Pacific - Room #3113, BC Children's Hospital

  • Wednesday, June 7 - Short read mapping and visualization
    9:30-11:30am Pacific - Room #3113, BC Children's Hospital

  • Thursday, June 8 - Variant calling - small variants
    10am-12pm Pacific - Room #2108, BC Children's Hospital

  • Friday, June 9 - Mid-Series Exam
    10am-12pm Pacific - Room #2108, BC Children's Hospital

  • Monday, June 12 - Variant Annotation
    10am-12pm Pacific - Room #3113, BC Children's Hospital

  • Tuesday, June 13 - RNA-seq read mapping
    10am-12pm Pacific - Room #3113, BC Children's Hospital

  • Wednesday, June 14 - RNA-seq II
    9:30-11:30am Pacific - Room #3113, BC Children's Hospital

A detailed syllabus can be found here.

Session Format:

  • Each session's timeslot will be divided into:
    • 45 minute lecture
    • 15 minute Q&A
    • 45 minute problem set
    • 15 minute wrap-up
  • The June 9 session will be used for a mid-series 'exam'

Who Should Attend:

  • Any research faculty, grad students, or university staff interested in learning the basic steps of genomic analysis using high performance computing resources.
  • The modular setup of the workshop series allows users of any skill level to attend, from those with zero experience in the linux shell, to experienced bioinformaticians eager to learn a new tool set.

Prerequisite Requirements:

  • You need a Compute Canada / WestGrid account to participate in this session, however, a guest account can be created for you if needed.
  • When you register for the session, please indicate if you require a guest account.

For more information on this session or if you have questions about the required skills or knowledge, please contact us.

Session Materials Archive

To access the slides, video recordings, problem sets, and other workshop materials, please visit:
https://phillip-a-richmond.github.io/Introduction-to-Genomic-Analysis/