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General introduction to Genome Variant Analysis (GVA14)

General introduction to Genome Variant Analysis (GVA14)

May 15, 2014

Overall Course Learning Objectives

  • Be capable of navigating a Linux operating system and TACC's Lonestar system in particular

  • Understand the biological questions, technologies, and workflows related to genome variant analysis, including:

    • Types of variants detectable by NGS

    • Terms: eQTL / GWAS / causative mutation analysis / population genetics

    • phylogenetics: evolution (e.g. quasi-species evolution), ecology (e.g. populations, pooled samples, bacterial communities)

    • Genotype / phenotype associations - either at a gross scale (e.g. mapping) or fine scale (e.g. causative mutations)

    • Technologies:

      • WGA

      • Exome

      • ddRAD

      • sequencing technologies

  • Related topics which are outside the scope of this course include: allele specific expression, methylation analysis, ChIP-seq, RIP-seq

Learning Objectives: Day 1, Part 1: Linux/TACC Introduction

  • Learn and practice essential Linux concepts and commands, including where to get more help & information

  • Learn and practice working with TACC systems (Lonestar in particular)

Other Resources: