This repository contains the Laboratory Exercises and Final Project performed for the Statistical Genomics course held in the frame of my PhD at Graz University of Technology (TU Graz).
The course provides knowledge of high throughput array and sequencing technologies and hands-on experience with the analysis of the data from various applications. Examples of applications are transcriptome sequencing (microarrays and RNA-seq), variant calling, and ChIP-seq.
Lab 1 Fundamentals of Molecular Biology and working with Unix systems
Lab 2 Data wrangling and visualization with R
Lab 3 Gene expression analysis with microarrays
Lab 4 Next-generation sequencing technologies
Lab 5 RNA-seq
Lab 6 ChIP-seq
Lab 7 ATAC-seq
Lab 8 MeDIP-seq
Lab 9 Hi-C
Lab 10 Genetic variation: SNPs and INDELs
Lab 11 Genetic variation: Structural and copy number variation
Final Project
Linux/Unix:
sratoolkit.3.0.2 \
Trimmomatic-0.39 \
hisat2-2.2.1 \
samtools-1.13
R 4.2.2:
tidyverse \
BiocManager 3.16 \
GenomicAlignments \
rtracklayer \
DESeq2