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ALBERTA EPIGENETICS NETWORK RNA-Seq, DNA methylation & Bioinformatics works...

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University of Lethbridge

4401 University Drive West

Lethbridge, AB T1K 6T5


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The Alberta Epigenetics Network (AEN) is organizing an RNA-Seq and DNA methylation (bisulfite-seq) bioinformatics workshop at the University of Lethbridge over the dates of March 29th – 31st, 2017. The workshop is being organized in conjunction with the AEN Annual Summit in Lethbridge on March 27 and 28, 2017.

The workshop is being run under the supervision of Dr. Igor Kovalchuk and will cover RNA-Seq and bisulfite-seq (DNA methylation) and the associated data analysis and is aimed at Graduate Students, PDFs, and any interested investigators from the Universities of Alberta, Calgary, and Lethbridge. The goal of the workshop is to introduce participants to the molecular techniques required for RNA-Seq and Bisulfite-Seq, computational tools required for processing the data and bioinformatics tools required to analyze these datasets.

Topics Include:

Molecular Techniques:

· Library Prep

· Library Validation

· Sequencing

Data Analysis

· Introduction to R, RStudio and Bioconductor

· Quality Control

· Mapping

· Annotation

· Data exploration

The workshop starts on Wednesday, March 29th, 2017

Provisional schedule for the workshop:

Day 1. 29.03.2017 (starts at 9.00 am)

Data analysis for RNA-sequencing projects

  • 09.00 – 09.15 am – Introduction to data analysis part of the workshop
  • 09.15 – 10.15 am – Intro to RNA-sequencing (lecture)
  • 10.15 – 10.30 am – Coffee break
  • 10.30 – 11.30 am – Review of some common RNA-sequencing scenarios (lecture)

Lab 1. Detection of differentially expressed genes (hands on part of the workshop)

  • 11.30 – 11.40 am – Short intro to hands-on part of the workshop. Organizational issues.
  • 11.40 – 01.00 pm – Getting familiar with Linux command line (hands-on)
  • 01.00 – 01.45 pm – Lunch
  • 01.45 – 03.30 pm – Sequencing library quality control, read mapping, visualizing alignments (hands-on and theory)
  • 03.30 – 04.30 pm – Obtaining read counts at the gene level (hands-on)

Day 2. 30.03.2017 (starts at 9 am)

Data analysis of RNA-sequencing projects

  • 09.00 – 10.30 am – Intro to R (hands-on)
  • 10.30 – 12.00 pm – Data exploration and detection of differentially expressed genes using R and Bioconductor (hands-on)
  • 12.00 – 01.00 pm – Lunch
  • 01.00 – 02.00 pm – Annotate the results of differential expression using R and Bioconductor (hands-on)
  • 02.00 – 04.30 pm – Pathway and GO term enrichment analysis for differentially expressed genes (hands-on and theory)

Day 3. 31.03.2017 (starts at 9 am)

Data analysis of DNA methylation analysis – bisulfite sequencing

Lab 2. Detection of differentially methylation regions (DMRs)

Schedule is TBD

  • 04.15 – 04.20 – Concluding remarks. End of the workshop.

For more information about the workshop and to register:

  1. Please email Dr. Igor Kovalchuk at
  2. Follow this link to Eventbrite site for registration
  3. Contact Alberta Epigenetics Network for assistance with travel and accommodation at


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University of Lethbridge

4401 University Drive West

Lethbridge, AB T1K 6T5


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