May 2013

Your Instructors

instructor action item list

Day 1a: Scott 1b: Jeff
Day 2a: Jeff, Daechan, Anna, 2b: Scott
Day 3a: Jeff 3b: Iyer lab
Day 4a: Jeff, 4b: Scott

Instructors: meet 9am Monday for final check

Each Part 1/Part 2 section needs to be standardized with:
*Learning Objectives
*Theory
*Workflow diagram (data, toolbox/recipe, exercises)
*Tutorial (bulk of time here)
*Recap learning objectives
*Next steps...

Day 1: Linux/TACC Introduction and Read Mapping

Part 1: Linux/TACC Introduction

• General introduction (SPHS)
  • Introduction to Bioinformatics Prezi
• Linux refresher (SPHS)
  • Step 1: Start somewhere
  • Step 2: Establishing a profile on Lonestar
  • Step 3: Editing files
  • Step 4: Final explanations
  • 
• Using TACC's Lonestar Cluster (SPHS)
  • Diagram of Lonestar's directories
  • 
  • Diagram of running a job on Lonestar
  • 
  • Using SFTP for file browsing on Linux.
• Recap and "for further study"

Part 2: Read Mapping

• Introduction to next-gen sequencing technologies (JB)
  • Paper comparing NGS technologies (Liu et al., 2012)
  • Official Illumina video | Another Illumina video
  • Broad Center GA Boot Camp
• Variant calling workflow diagram:
• (JB)
• Mapping tutorial (bowtie, BWA, bowtie2) (JB)
• Integrative Genomics Viewer (IGV) tutorial (JB)
• Tutorial - Start diploid mapping for Day 2

Enrichment modules (4:30-5:30)

• Sharing Linux tricks - linux one-liners (SPHS)
• Working on TACC from your Mac or PC (AB)
  • Editing files, more detail

Extras

• Running Unix & Perl for Biologists tutorial at TACC
• Installing Virtual machine & Linux on Windows (DP)

Day 2: Examining Raw and Aligned sequences, and Calling Genome Variants

Part 1. Examining Raw and Aligned sequences

• Evaluating your raw sequencing data (DP/AB)
  • GSAF adaptor and barcode sequence resource
• Mapped read data evaluation (SAMtools) (DP/AB)
• Practical advice - Final odds & ends for short read re-sequencing data

Part 2. Calling Genome Variants

• Example genome variant calling pipeline (SPHS)
  • Variant calling workflow diagram:
• Introduction to genome variation
• (SPHS)
• Variant calling tutorial (SAMtools) (SPHS)
• Calling variants in diploid genomes (SPHS)

Enrichment module (12:30-1:30)

• Shell Scripting (SPHS/AB)

Enrichment modules (4:30-5:30)

• Installing Linux tools (JB)

Extras

• Variant calling with GATK (SPHS)
• Annotating variants (SPHS)
• (JB)
• Visualize mapped data at UCSC genome browser (AB)
• Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
• Identifying structural variants (SVDetect) (JB)
• SRA toolkit (AB)

Day 3: RNA-seq

Part 1. Introduction to RNA-seq Counting

• 
• Differential gene expression analysis (JB)

Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)

• Differential expression with splice variant analysis

Enrichment module (12:30-1:30)

• Identifying mutations in microbial genomes (breseq) (JB)

Enrichment modules (4:30-5:30)

• Start tophat by submitting to lonestar (DA)

Extras

• Visualize mapped data at UCSC genome browser (AB)
• non-coding RNA analysis

Day 4: Assembly and Annotation

Part 1. Genome Assembly

• 
• Genome Assembly Examples (SPHS)
• Tutorial: Genome Assembly (velvet) (SPHS)

Part 2. Assembly Annotation

• Genome Annotation (Glimmer3) (VR)
• Evaluating & Visualizing assemblies (bacterial)

Enrichment module (12:30-1:30)

• Office hours: "I want to learn how to install and use this tool called ______ that we didn't talk about in class." (JB).

Enrichment module (4:30-5:30)

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

Resources

• Scott's list of linux one-liners
• Example BWA alignment script
• Exercises
• Key take home points

Resources tool list, file formats & more

As you're getting settled