RNAseq data analysis


13 - 16 March 2023

This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of online lectures and computer practicals.

Audience National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS).

Fee 1800 SEK (for academic participants, please contact us for more information on the non-academic fee). Please note that NBIS cannot invoice individuals. The fee covers lunches, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. 

Note that travel and accommodation is not included in the fee and must be arranged by the participants. 



Covered topics

  • RNAseq Quality control analysis
  • Mapping of short reads
  • Quantification of gene expression
  • Exploratory data analyses
  • Differential gene expression
  • Gene set enrichment analysis



The final day for application has passed, no more applications will be accepted. Next instances of this course will be announced on the NBIS http://nbis.se/training/events.html and SciLifeLab https://www.scilifelab.se/education/courses/ websites.

This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff. We do accept application from other countries, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Entry requirements

Required for being able to follow the course and complete the computer exercises:

  • Basic knowledge in Linux and R
  • Your own laptop with the following specs:
    • At least 6 GB of RAM. 
    • Operating system Win10, OS X or Linux
    • At least 30 GB of free storage


  • Experience working with NGS data analysis or completed the NBIS workshop “Introduction to Bioinformatics using NGS data”
  • Experience working in R or completed the NBIS course “R Programming Foundations for Life Scientists”

Due to our best practice to have a high teacher to student ratio we have set the number of participants to a maximum of 22 participants. If we receive more applications, 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.


travel-location.svg Course location

Entrance C11,
Biomedical Centre (BMC) / SciLifeLab
Uppsala University
Husargatan 3,
752 37 Uppsala

Use the UL website or the UL app for bus and train services around Uppsala. 

To find the room within BMC, enter via C11 and see https://link.mazemap.com/DcIYaHIo

The door will be open every day between 8:30 and 9:00.



Course schedule can be found on this page: Schedule


Precourse material

Please read carefully the Pre-course instructions material before the course start. If you have any problems with pre-course installations, please ask your questions in Installation and pre-course related issues.



Youtube videos

RNASeq workshop videos


Course evaluation


Course staff

Course Leaders: Johan Reimegård, Julie Lorent, Nima Rafati


CC attribution share alike This course content is offered under a CC attribution share alike license. Content in this course can be considered under this license unless otherwise noted.