NOTE: as of August 2012 course material from each SSC course will be archived by course date. The links below are for the May 2012 course. You will find other course dates on the main BioIteam page.

Table of Contents:

Day 1: Linux/TACC Introduction and Read Mapping

• Linux refresher
• Using TACC's Lonestar cluster
• Introduction to mapping (bowtie, BWA)
• Introduction to variant calling (SAMtools)

Extras

• Introduction to Bioinformatics Prezi
• Download Presentation on Mappers, etc.
• Workflow diagram of variant calling
• Diagram of Lonestar's directories
• Diagram of running a job on Lonestar

Day 2: Calling Genome Variants

• Using the Integrative Genomics Viewer (IGV)
• Shell Scripting
• Mapped read data evaluation (SAMtools)
• Installing Linux tools
• Identifying mutations in microbial genomes (breseq)

Extras (come early Day 3)

• Calling variants in diploid genomes
• Annotating variants

Additional topics

• Variant calling with GATK
• Genome variation in mixed samples (FreeBayes, deepSNV)
• Identifying structural variants (SVDetect)

Even More Extras

• Download presentation on Advanced Genome Variant Calling
• Practical advice - short read re-sequencing data

Day 3: RNA-seq

• Differential gene expression analysis
• Differential expression with splice variant analysis
• Transcriptome assembly & annotation

Extras

• non-coding RNA analysis

Day 4: Assembly and Annotation

• Genome Assembly
• Genome Assembly (velvet)
• Genome Annotation (Glimmer3)
• Evaluating & Visualizing assemblies
• SRA toolkit, UCSC Genome Browser
• Custom Genome Databases

Resources

• Resources: tool list, file formats & more
• Scott's list of linux one-liners
• Example BWA alignment script
• Exercises