Content_URPP_Tutorials.md

URPP Tutorials

Stefan Wyder & Heidi Lischer

Bash shell (3parts 3x3h)

1. Basics 1 Folder structure, commands with files&folders, commands with text, piping, (awk)
2. Basics 2 ssh, compression, permission, (bash scripting)
3. Bash scripting bash scripting, parallelizing, awk, regexps

NGS (4parts, 4x3h)

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

R (2parts, 2x6.5h)

1. Introduction into 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