August 2012

http://www.broadinstitute.org/igv/projects/downloads/IGV_2.1.21.zip

Your Instructors

instructor action item list

Day 1: Linux/TACC Introduction and Read Mapping

• 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/AR)
  • Diagram of Lonestar's directories
  • 
  • Diagram of running a job on Lonestar
  • 
  • Using SFTP for file browsing on Linux.
• Introduction to next-gen sequencing technologies (SPHS)
  • Official Illumina video | Another Illumina video
  • Broad Center GA Boot Camp
  • GSAF adaptor and barcode sequence resource
• Application: Example genome variant calling pipeline (JB)
  • 
• Evaluating your raw sequencing data (JB/AB)
• Introduction to Mapping and Tutorial
  • (JB)
• Tutorial - Start diploid mapping for Day 2

Enrichment modules (4:30-5:30)

• Sharing Linux tricks (SPHS)
• Making it easier to work on TACC from a Mac (JB)

Extras

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

Day 2: Calling Genome Variants

• Mapping tutorial (bowtie2, BWA) (JB/GC)
• Introduction to genome variation
• (JB)
• Variant calling tutorial (SAMtools) (JB)

Enrichment module (12:30-1:30)

• Installing Linux tools (JB)

Enrichment modules (4:30-5:30)

• Shell Scripting (SPHS/AB)

Extras

• Calling variants in diploid genomes (SPHS)
• Variant calling with GATK (SPHS)
• Annotating variants (SPHS)
• (JB)
• Visualize mapped data at UCSC genome browser (AB)
• Mapped read data evaluation (SAMtools) (SPHS, DP)
• Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
• Identifying structural variants (SVDetect) (JB)
• Practical advice - short read re-sequencing data
• SRA toolkit (AB)

Day 3: RNA-seq

• Integrative Genomics Viewer (IGV) tutorial (JB)
• 
• Differential gene expression analysis (JB)
• Differential expression with splice variant analysis

Enrichment module (12:30-1:30)

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

Possible Enrichment modules (4:30-5:30)

• Start tophat by submitting to lonestar (DA)
• Visualize mapped data at UCSC genome browser (AB)
• Mapped read data evaluation (SAMtools) (SPHS, DP)

Extras

• non-coding RNA analysis

Day 4: Assembly and Annotation - Bacterial

• 
• Genome Assembly Examples (SPHS)
• Tutorial: Genome Assembly (velvet) (SPHS)
• Genome Annotation (Glimmer3) (VR)
• Evaluating & Visualizing assemblies (bacterial)

Enrichment module (12:30-1:30)

• "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

Extras

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