GS Bioinformatics 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)
- How to login to Cloud
- Brief introduction to Unix

Tuesday

Data pre-processing
Sequence alignment
Computer exercises: Galaxy sequence alignment
- Exercises
- Screenshots
Computer exercises introduction to R (self study):
- Torfs & Brauer: A (very) short introduction to R

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)
  - NicBar-Variants (xlsx)
  - Filter-Script (R)
- TEQC

Thursday

Neuroblastoma
Introduction into R2: Genomics Analysis and Visualization Platform (r2.amc.nl)
- Exercises

Friday

RNA sequencing
- Slides
- Exercises
- Answers
- R code
scRNA sequencing (slides)
Closing:
- Bioinformatics courses: https://www.biosb.nl/
- Phylogenetics analysis of the Corona virus: https://nextstrain.org/ncov

top