Lectures and presentations delivered during HTS Summer School

Reference and code sheets:

Introduction to Unix/Linux   *

Introduction to R   *

Introduction to High Throughput Sequencing  

HTS Data Formats and Quality Control  

Introduction to Statistical Concepts  

Mapping strategies for sequence reads (with focus on RNA sequencing)  

Transcript expression estimation, normalisation, differential expression analysis  

Sequence Alignment/Map Format Specification  

Analysis of Human Genome Variation  

Variant calling - Detecting variants in NGS data  

Variant Call Format  

Short Read Alignments  

Bash and IPython Notebook  

eQTL Mapping  

Statistical Challenges of Identifying the Genetic Determinants of Rare Diseases  

*Note that not all commands in the exercises will work unless the data files that werSequence Alignment/Map Format Specificatione used during the summer school are accessible.