RNA-seq Analyses in non-model organisms

dates

 

11-15 November 2019

 

Where

Here is the full address of our classroom: Profund Innovation, Freie Universität Berlin - Altensteinstraße 40, 14195 Berlin, Germany (http://tiny.cc/lijd5y)

 

Course overview

RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms. This workshop provides an overview of modern applications of transcriptome sequencing and popular tools and algorithms for exploring transcript reconstruction and expression analysis in a genome-free manner, leveraging the Trinity software and analysis framework. Attendees will perform quality assessment of Illumina RNA-Seq data, assemble a transcriptome using, among others, Trinity, quantify transcript expression, leverage Bioconductor tools for differential expression analysis, and apply Trinotate to functionally annotate transcripts. In parallel to the short-read assembly, participants will perform the pre-processing of 3rd generation sequencing data (PacBio IsoSeq) and the resulting assemblies will be compared. Additional methods will then be explored for characterizing the assembled transcriptome and revealing biological findings.

Intended audience

This workshop is aimed primarily at biologist researchers that have basic bioinformatics skills and are pursuing RNA-Seq projects in non-model organisms. Attendees will gain skills needed to successfully approach transcriptome sequencing, de novo transcriptome assembly, expression analysis, and functional annotation as applied to organisms lacking a high quality reference genome sequence. Attendees are also invited to bring a subset of their own data.

 

Teaching format

The workshop will be delivered over the course of four and a half days, with each session entailing lectures followed by practical hands-on sessions. Most computing will be done on the cloud and attendees will use their own laptop computers with the Google Chrome web browser providing all the necessary interfaces to the cloud computing environment, including the linux command terminal. Attendees can also use the native terminal emulator of their Operating System (and ssh). This works natively for Linux, MAC and Windows 10. For Windows 7 users, installing MobaXTerm would be recommended.

 

Assumed background for the participants

Basic experience with linux command-line execution and execution of bioinformatics tools would be helpful. We will begin the course with a review of basic linux commands and operations as a refresher. No programming or scripting knowledge is required.

 

Program

 

Monday – Classes from 09:30 to 17:30

* Session 1- Intro to the RNA-Seq de novo assembly workshop
* Intro to RNA-Seq, Next-gen sequence analysis and the workshop setup

* Practical: exploring the computational infrastructure

* Session 2- Read quality assessment and trimming

* Practical: using FASTQC, TRIMMOMATIC, MultiQC

* Session 3- Short Read de novo assembly

* Overview of de novo transcriptome assembly

* Practical: assemble rna-seq data using ORP

 

Instructors

Dr. Nicolas Delhomme

 

 

 

 

 

 

 

 

Bastian Schiffthaler

 

 


Cost overview

 

Package 1

Course and refreshments

 

          530 € (VAT included)


Please click HERE to get all the information about our packages.

Cancellation Policy:

 

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.