NGS - Single-cell RNA-Seq Analysis

Date 28 - 29 November 2019
Speaker(s) Walid Gharib
Fees *academic: 120 CHF   -   for-profit: 600 CHF
Cancellation deadline 14 Nov 2019
City Bern
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


In contrast to the Bulk RNA sequencing used to quantify the abundance of gene and transcript expression at a whole population level, single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression profile at a single cell resolution while enabling the discovery of tissue specific sub populations and markers. For example, contrasting different sample conditions i.e. disease vs. normal using scRNAseq can help identify sub-cellular differential behaviours and thus target specific gene markers. This 2-days course will cover the main technologies as well main aspects to consider while designing a scRNAseq experiment including a hands-on practical data analysis session applied to droplet-based methods.


First day

Introduction to scRNAseq:

  • Technologies
  • Experimental design

Quality control

  • Dropouts - Doublets
  • Ribosomal / mitcochondrial RNAs

Normalization and scalability

  • Feature selection
  • Log scaling
  • confounding factors removal

Second day

Dimentionality reduction and cell type clustering

  • PCA
  • tSNE
  • UMAP
  • Clustering methods (Hierarchical, K-means and Graph-based)

Differential expression analysis

  • Methods overview
  • DE between clusters
  • DE between samples (involving data-integration)

Cell type identification

  • Methods and applications

Pseudotime analysis

  • Methods and applications


This course is intended for life scientists and bioinformaticians familiar with "Next Generation Sequencing" who wish to acquire the necessary skills to analyse scRNA-seq gene expression data.

Learning objectives

At the end of the course attendees will be able to:

  • distinguish advantages and pitfalls of scRNAseq
  • design their own scRNA-seq experiment
  • apply a downstream analysis using UNIX and R

Knowledge / competencies prerequired (Mandatory)

Participants should already have a basic knowledge in Next Generation Sequencing (NGS) techniques, or have already followed the "NGS - Quality control, Alignment, Visualisation" given twice a year at the SIB. Knowledge in RNA sequencing is a plus. A basic knowledge of the R statistical software and completion of an introductory course on UNIX (eg UNIX fundamentals) or equivalent knowledge is also required.

Technical requirements

A Wi-Fi enabled laptop.


Applications will open 2 months before the course starts.

Registration fees are 120 CHF for academics and 600 CHF for for-profit companies. This includes course content material and coffee breaks.

Deadline for registration and free-of-charge cancellation is set is set to 14/11/2019. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

University of Bern, Hochschulstrasse 4 (main building of the University of Bern), classroom 304, 3. OG Ost.

The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants on due time.

Additional information

Coordination: Patricia Palagi, SIB Training Group

Trainer: Walid Gharib, SIB Training Group & IBU

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact