This course is suited for beginners in Bioinformatics with very little prior knowledge. Its objective is to teach scientists working with NGS data the basic skills to write their own Python scripts to handle their data.
The course will be focused on direct application of the learned techniques in hands-on labs. Basic knowledge of working with the command line is advantageous, but not a prerequisite.

Resources

Preparation

In order to prepare your computer for the course please follow this guide and afterwords test your Python setup with these scripts: Windows and Linux/MAC.

If you have any questions or problems please write an email to Felix Heeger.

Day 1 (Monday)

Chapter 1: Text output and manipulation

Slides

Solutions: ex1-1 ex1-2 ex1-3 ex1-4 ex1-5

Chapter 2: Reading and writing files

Slides

Exercise: genomic_dna.txt

Solutions: ex2-1 ex2-2 ex2-3

Day 2 (Tuesday)

Chapter 3: Lists and loops

Slides

Exercise: ex3-1_input.txt ex3_genomic_dna.txt exons.txt

Solutions: ex3-1 ex3-2

Chapter 4: Writing your own functions

Slides

Solutions: ex4-1 ex4-2

Day 3 (Wednesday)

Chapter 5: Conditional statement

Slides

Exercises: data.csv

Solutions: ex5-1 ex5-2

Chapter 6: Dictionaries

Slides

Exercises: dna.txt translation.txt

Solutions: ex6-1

Day 4 (Thursday)

Chapter 7: Files, programs and user input

Slides

Exercise: dna.zip

Solutions: ex7-1 ex7-2

Chapter 8: Biopython

Slides

Exercise: sample1.fq reads.fq

Solutions: ex8-1 ex8-2 (Note: ex8-2 was not done during the course)

Day 5 (Friday)

Hands on training on participant problems

  1. Sub-sampling NGS reads
    Solution: subsampling
  2. Determining sequence frequency in NGS data
    Solution: sequenceFrequency
  3. Finding orthologous proteins between different bacteria