RNA-seq, 1 hp


A national course open for PhD students, postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Application form

Important dates

Application open: In the beginning of August

Application deadline: September 17

Conformation to accepted students: September 24

Responsible teacher: Johan Reimegård

If you don’t receive information according to the dates above, contact eva.molin@scilifelab.uu.se

Course fee

A course fee of 1000 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner).

Workshop content

This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in the RNA-seq and biostatistics will cover a range of cutting-edge issues in different RNA-seq applications, including updates on long reads sequencing and single-cell sequencing. An extensive case study in the computer lab will familiarize you with concepts of mapping, de novo assembly, differential expression analysis and different aspects of quality control of your RNA-seq data.

Topics covered will include:

* Gene and isoform detection using short RNA-seq reads
* Gene and isoform detection using long RNA-seq reads
* Gene and isoform detection combining RNA-seq data with other data sources
* Quality assessment of RNA-seq data
* Differential expression analysis using RNA-seq data on multiple cells
* Gene detection and differential expression analysis using RNA-seq data on single cells

Entry requirements

* Basic knowledge in Linux is a requirement! We will not teach Linux at the course, and you will have considerable trouble to follow the practical sessions if you are not reasonably used in a Linux environment.
* Be able to bring your own laptop for the practical computational exercises. If you don’t have a laptop to bring, please contact Eva Molin, eva.molin@scilifelab.uu.se before you register.
* Some programming/scripting experience is desirable, but not required.
* Experience working on the SNIC center Uppmax is desirable, but not required.
* Participants of the SciLifeLab course “Instroduction to Bioinformatics using NGS data” (or like) are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the course will be considerably more detailed on the covered topics.

Due to space constraints for the computer exercises, there are a maximum number of participants allowed. If we receive more applications than places available, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.