Bioinformatics for Sequence Analysis
Links
Image: wikipedia “DNA sequencing”
Schedule and handouts
- Schedule2021 (pdf, last update: 04-03-2021)
The lectures are in Zoom and the computer exercises in Discord (unless told otherwise). The links were sent around by mail.
Monday
- Introduction
- Sequencing techniques
- Computer exercise: Introduction sequence databases
- Computer exercises: Introduction Unix/Linux (self study)
Tuesday
- Data pre-processing
- Sequence alignment
- Computer exercises: Galaxy sequence alignment
- Computer exercises introduction to R (self study):
Wednesday
- Exome sequencing (Antoine van Kampen, Barbera van Schaik)
- Presentation (Details; pptx)
- Computer Exercises
- Cloud Instructions
- Use “Method 2”, starting at “Step 3”
- You also need to add this to the Putty settings: Connection > Proxy: http, proxy.amc.nl, 3128
- Ip-address is: 145.100.58.134
- Exercises (pdf)
- TEQC
Thursday
- Neuroblastoma
- Introduction into R2: Genomics Analysis and Visualization Platform (r2.amc.nl)
Friday
- RNA sequencing
- scRNA sequencing (slides)
- Closing:
- Bioinformatics courses: https://www.biosb.nl/
- Phylogenetics analysis of the Corona virus: https://nextstrain.org/ncov
