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Transcriptomics Workshop

Friday 2nd - Saturday 3rd October 2015 (Program)

A 2-day beginners-level workshop for analysis of transcriptomes will be held at La Trobe University as a satellite to the 2015 Melbourne ComBio conference.

  • RNA-seq Overview
  • Read mapping
  • Gene expression counting
  • Differential expression analysis
  • De-novo transcriptome assembly

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Overview

A 2-day beginners-level workshop for analysis of transcriptomes will be held at La Trobe University as a satellite to the 2015 Melbourne ComBio conference.

This workshop is designed to teach the fundamental skills to map or de novo assemble RNA-seq data and basic differential expression analysis.

Attendance at the workshop is limited to 25 places.

We will have an introduction to RNA-seq experimental design, and learn the basics of mapping to a reference genome and counting gene transcripts, de novo assembly for non-model organisms, and preliminary differential expression analysis.

This workshop will run in a Unix environment. However, no prior Unix experience is required.

Workshop participants are welcome to bring their own next-generation transcriptome data, which they may move onto later in the second day.

The workshop will be led by Nathan Hall, a senior bioinformatician at La Trobe University and VLSCI.

Program Committee:

Where:
LIMS Computer Lab 308, La Trobe University (Map)
What to bring:
Laptop (optional)
Transcriptome Data (optional)
Registration:
Closes 26th June 2015 (Register)
Cost:
$50 (to help cover Catering and IT Services)

Program

Friday 2nd October

  • 09:00 - 10:00: Welcome, Course overview and Introductions
  • 10:00 - 10:45: Transcriptomics overview
  • 10:45 - 11:15: Break
  • 11:15 - 11:45: Assessing read quality with FastQC
  • 11:45 - 12:30: Mapping reads to a reference genome with Tophat/Bowtie
  • 12:30 - 13:30: Lunch
  • 13:30 - 14:15: Read counting for gene expression with HTSeq-count
  • 14:15 - 15:30: Determining differential gene expression with Degust
  • 15:30 - 16:00: Break
  • 16:00 - 17:30: Determining differential gene expression with Degust cont.
  • 17:30 - 18:30: Drinks

Saturday 3rd October

  • 09:00 - 10:30: Transcriptome assembly with Trinity
  • 10:30 - 11:00: Break
  • 11:00 - 12:00: Assembly analysis with Blast
  • 12:00 - 13:00: Lunch
  • 13:00 - 14:30: Own project and discussion

Register

Workshop Application

Applications close Friday 10th July 2015, limited to 25 places

There is a $50 attendance fee, payable when accepting a place, to help cover catering and IT services

NOTE: Registering your interest does not guarantee you a place at this workshop

Places will be confirmed via email by Tuesday 14th July 2015

Accommodation

The workshop is on during the AFL grand final weekend which will make it difficult to find reasonably priced accommodation. We have secured accommodation at La Trobe Apartments at standard rates during the workshop within 10 mins walk of workshop venue.

There are a number of single and shared accommodation options on-hold at La Trobe Apartments.

You will need to make your own accommodation arrangements.

To book on campus accommodation contact Accommodation Services directly and quote Transcriptome Workshop

Rates: Apartments

Phone: +61 3 9479 1071

Email: living@latrobe.edu.au

Contact / Location

Contact: Nathan Hall (n.hall@latrobe.edu.au) for any workshop related queries.

Course Location: LIMS Computer Lab 308

Accommodation: La Trobe University Apartments