Contents

Workshop learning materials. Slides: / , Labs: , Videos:
Note

Note that the slides and videos may not be in sync because the slides were updated while the videos are from previous workshops.

Topic Presenter Links
Introduction to Linux Martin Dahlö Video Slides Lab
Linux file permissions Martin Dahlö Lab
Introduction to HPC Martin Dahlö Video Slides Lab
HPC pipelines Martin Dahlö Lab
File types in Linux Martin Dahlö Video Slides Lab
Better terminal experience Martin Dahlö Video Slides
QC of FastQ reads Marcel Martin Slides Lab
Advanced Linux Martin Dahlö Video Slides Lab
NGS technologies and challenges NGI Video Slides
NGS long reads and pipelines NGI Video Slides
Variant-calling workflow Diana Ekman Video Slides Lab
RNA-Seq workflow Roy Francis / Dag Ahrén Video Slides Lab
Data management NBIS DM Video Slides

Useful resources

  • Connecting to HPC PDC
  • Connecting to HPC UPPMAX
  • Uploading & downloading files from HPC
  • Using X11 on Windows with VcXsrv
  • Simon’s RNASeq analysis
  • Linux cheatsheet
  • Bash cheat sheet 1
  • Bash cheat sheet 2
  • Bash cheat sheet 3
  • Uppmax cheatsheet
  • Mac keyboard