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

Day 1 followup
Daechan original shell scripting page