dates

11th-15th December 2023

To foster international participation, this course will be held online

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.

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. Familiarity with Linux and the bash shell are strongly recommended.

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.

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.

Monday – Classes from 2-8 pm Berlin time

* 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