URPP Tutorials

URPP Evolution in Action

Stefan Wyder & Heidi Lischer

1. Introduction to Linux and bash scripting

2. Next-Generation-Sequencing (4 parts, see below)

3. Introduction to R

4. Introduction to Python

5. Version control (git)

6. NGS analysis utilities

7. Phylogenetic trees/Phylogenomics

8. Genomic data visualization / Genome browsers

9. Principles of data visualization

Detailed overview

Linux/Bash shell (3 parts, 3x3h=9h)

1. Basics 1
   Folder structure, commands with files&folders, commands with text, piping, (awk)
   Hands-on
2. Basics 2
   ssh, compression, permission, (bash scripting)
   Hands-on
3. Intermediate
   • bash scripting | Exercises
   • parallel jobs, awk, regexps | Hands-on

Next-Generation-Sequencing (4 parts, 4x3h=12h)

1. Introduction
   Sequencing Technologies, Quality control (FastQC), SAM/BAM formats, samtools
   Hands-on
2. Variant Calling
   Preprocessing BAMs, variant calling example (freebayes), VCF format
   Hands-on
3. Variant Calling 2
   variant calling (GATK), Variant Effect Prediction
   Theory 1 | Theory 2 | Hands-on
4. RNA-seq & Making sense of gene lists
   Differential expression (edgeR), Gene Ontology Analysis, Gene Set Enrichment Analysis
   Theory 1 | Theory 2 | Hands-on 1 | Hands-on 2

R (3 parts, 2x6.5h+3h=15h)

1. Introduction to R
   Using R as a calculator, variables, subsetting, reading in data, writing functions, apply functions, missing data, plotting (base::plot)
2. Programming Exercises
   Plotting using ggplot2, writing clean code, programming exercises
3. Programming Exercises 2
   Repetition (programming structures, clean coding, project organization)

website

Introduction to python (2 parts)

1. Basics
   Basics, control flow, lists, file input/output, writing function, dictionaries, tuples, sets
2. Basics 2*
   Object-oriented programming, BioPython, regular expressions

website