De novo Transcriptome assembly - Trinity

Date 10 - 11 October 2016
Speaker(s) Broad Institute: Brian Haas, Timothy Tickle
Requirements Basic Unix knowledge is mandatory
Basic R-statistics knowledge is recommended
ECTS 0.5
Fees *academic: 100 CHF   -   for-profit: 0 CHF
Cancellation deadline 7 Oct 2016
City Bern
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


Through a combination of lecture materials and hands-on computational exercises, we explore the use of Trinity for de novo rna-seq assembly and downstream analysis of transcript expression, annotation, differential expression, and interactive data analysis. Although participants will be provided with sample RNA-Seq data sets, they are encouraged to bring their own data for use during the guided studies. We can also include information on applications for cancer transcriptome studies and/or studies of non-model organisms lacking reference genomes.

Invited lecturers:

  • Brian Haas, Broad Institute, Cambrigde, USA
  • Tim Tickle, Broad Institute, Cambrigde, USA

Learning objectives

Attendees will learn how to use the Trinity framework for de novo transcriptome assembly and downstream analysis, including quality assurance, transcript quantification, differential expression, and functional annotation. The workshop will consist of a combination of lecture and hands-on workshop activities to gain familiarity with the various tools utilized, including the Trinity assembler and Bioconductor packages.

Bring your own data (optional attendance):

Friday 14th of October is a great opportunity for the participants of the "Single Cell sequencing" and "De novo Transcriptome assembly" workshops to bring their own data and start their analysis onsite and/or ask questions concerning their own research expermiental design.

Location: Room 331 3.OG/West, University of Bern, Hochschulstrasse 4, Bern, Switzerland (MAP)

Registration for this day is free of charge but mandatory, the first 30 registrations will be accepted for attendance (room space allowance):

Bring your own data registration here


Knowledge / competencies:

Attendees should already be familiar with the basic terms and concepts of genetics and genomics.


Attendees should bring their own laptop computers.

For the practical tutorial, basic familiarity with the command line environment is required.

Prior to the course, please download the Integrative Genome Viewer (IGV).

Schedule overview

Day 1:
Morning: Intro to RNA-Seq and transcriptome analysis
Afternoon: De novo transcriptome assembly

Day 2:
Morning: Transcript expression quantification and differential expression
Afternoon: Transcript clustering and functional analysis


Room 331 3.OG/West, University of Bern
Hochschulstrasse 4, Bern, Switzerland (MAP)

Additional information

Organizer: Walid Gharib, Training Group – Swiss Institute of Bioinformatics & IBU - Interfaculty Bioinformatics Unit - University of Bern

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