Detailed information about the course
De novo RNA-Seq assembly workshop
25-26 June 2018
|Lang||Workshop language is English|
|Responsable de l'activité||
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.
Day 1: (beginning at 9:15)
Morning: Intro to RNA-Seq and transcriptome analysis
Afternoon: Expression Quantitation and Assembly Quality Assessment
Day 2: (beginning at 9:15)
Morning: Differential expression analysis
Afternoon: Transcript functional annotation and DE cluster functional enrichment studies
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.
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.
|Deadline for registration||15.06.2018|
Dr. Walid Gharib, Training Group – Swiss Institute of Bioinformatics & IBU - Interfaculty Bioinformatics Unit - University of Bern