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)
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
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