August 2012

instructor action item list

Day 1: Linux/TACC Introduction and Read Mapping

• General introduction (SPHS)
  • Introduction to Bioinformatics Prezi
• Getting started at TACC
• Linux refresher (SPHS)
  • 
• Using TACC's Lonestar Cluster (SPHS)
  • Diagram of Lonestar's directories
  • 
  • Diagram of running a job on Lonestar
  • 
• Introduction to next-gen sequencing technologies
  • Official Illumina video | Another Illumina video
  • Broad Center GA Boot Camp
  • GSAF adaptor and barcode sequence resource
• Application: Example genome variant calling pipeline
  • 
• Evaluating your raw sequencing data (JB/AB)
• Introduction to Mapping and Tutorial
  • (JB)
  • Mapping tutorial (bowtie2, BWA) (JB/GC)
• Integrative Genomics Viewer (IGV) tutorial (Part 1) (JB)
• start diploid mapping (copy from Day 2 content)

Enrichment modules (4:30-5:30)

• Installing Linux virtual machine on Windows (DP)
• Sharing Linux tricks (SPHS)

Extras

• Running Unix & Perl for Biologists tutorial at TACC

Day 2: Calling Genome Variants

• Introduction to genome variation
• (JB)
• Variant calling tutorial (SAMtools) (JB)
• Integrative Genomics Viewer (IGV) tutorial (Part 2) (JB)
• Visualize mapped data at UCSC genome browser (AB)
• (JB)
• Calling variants in diploid genomes
• Variant calling with GATK
• Annotating variants (SPHS)

Enrichment modules (4:30-5:30)

• samtools tricks (DP)
• Installing Linux tools (JB)
• Shell Scripting (SPHS/AB)

Extras

• Mapped read data evaluation (SAMtools) (SPHS)
• Genome variation in mixed samples (FreeBayes, deepSNV)
• Identifying structural variants (SVDetect)
• Practical advice - short read re-sequencing data
• SRA toolkit, more UCSC Genome Browser

Day 3: RNA-seq

• Intro materials - (SPHS - JB/DA)
• Differential gene expression analysis (JB - bedtools & R)
• Differential expression with splice variant analysis
• MvA, volcano, heat maps, maybe goseq (R), cumberbund - check R version (SPHS/DA)

Enrichment module (12:30-1:30)

• Identifying mutations in microbial genomes (breseq)

Enrichment module (4:30-5:30)

• Start tophat via script (DA)

Extras

• non-coding RNA analysis

Day 4: Assembly and Annotation - Bacterial

• Genome Assembly (SPHS - add intro material)
• Genome Assembly (velvet) (SPHS)
• Genome Annotation (Glimmer3) (VR)
• Evaluating & Visualizing assemblies (bacterial)

Enrichment module (4:30-5:30)

• Transcriptome assembly & annotation
• Protein functional classification...
• Custom Genome Databases

Extras

Resources

• Scott's list of linux one-liners
• Example BWA alignment script
• Exercises

Resources tool list, file formats & more