GS Bioinformatics Sequence Analysis

Links

Image: wikipedia “DNA sequencing”

Schedule and handouts

Schedule2020 (pdf)

Monday

Introduction
Sequencing techniques
Computer exercises: Introduction
- C3ND (Windows)
- C3ND (MacOSX)

Tuesday

Data pre-processing
Sequence alignment
Computer exercises: Galaxy sequence alignment
- Exercises
- Screenshots
Computer exercises: Introduction Unix/Linux
- Command-line bootcamp
- Brief introduction to Unix

Wednesday

- RNA sequencing
  - Slides
- Neuroblastoma
- Introduction into R2: Genomics Analysis and Visualization Platform (r2.amc.nl)
  - Exercises
- Computer exercises: Torfs Brauer Short R Intro

Thursday

Exome sequencing (Antoine van Kampen, Barbera van Schaik)
- Presentation (Principles, 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: 145.100.57.228
  - Exercises (pdf)
  - NicBar-Variants (xlsx)
  - Filter-Script (R)
  - TEQC

Friday

scRNA sequencing (slides)
RNA sequencing
Immunology

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