De novo RNA-Seq assembly workshop

25-26 June 2018

Rémy Bruggmann

Dr. Gharib Walid, UNIBE & SIB

Mr. Brian Haas, Broad Institute, Cambridge, USA (senior computational biologist)

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.

Schedule overview

Day 1: (beginning at 9:15)

Morning: Intro to RNA-Seq and transcriptome analysis

• lecture on intro to rna-seq and the Trinity algorithm for transcript reconstruction
• practical: evaluation of NGS read quality
• practical: in silico normalization of reads
• practical: trinity assembly

Afternoon: Expression Quantitation and Assembly Quality Assessment

• lecture on expression quantitation
• practical: using RSEM and kallisto for expression quantitation
• practical: evaluating transcript assembly quality

Day 2: (beginning at 9:15)

Morning: Differential expression analysis

• lecture on differential expression analysis and the importance of statistics
• practical: using edgeR to identify DE transcripts and genes
• practical: transcript clustering

Afternoon: Transcript functional annotation and DE cluster functional enrichment studies

• lecture on transcript functional annotation
• practical: using Trinotate to functionally annotate transcripts and genes
• practical: using goseq to identify functional enrichments of DE clusters

For more details, please contact: Dr. Walid Gharib

UNIBE, Hochschulstrasse 4, room Nr. 028 / EG West

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): It 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 experimental design.

Prerequisites:Knowledge / competencies:

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

Technical: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)

This course is free to CUSO PhD students. Participants who are not CUSO PhD students will be charged CHF 120.-.

You will be informed by email of your registration confirmation.

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