NOTE: as of August 2012 course material from each SSC course will be archived by course date. The links below are for the May 2012 course. You will find other course dates on the main BioIteam page.

Table of Contents:

instructor action item list

http://loving.corral.tacc.utexas.edu/bioiteam/ which links to $BI/web

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
  • Cluster
    • Diagram of Lonestar's directories
    • Diagram of running a job on Lonestar
• Introduction to mapping (bowtie
  • Evaluating your raw sequencing data
  • Alignment withbowtie,BWA (JB/GC)
    • Download Presentation on Mappers, etc.|^NGS+class 22Mar12.
  Introduction to variant calling (SAMtools
  • • ppt|||||||||
• Using the Integrative Genomics Viewer (IGV) (JB)
  • Workflow diagram of variant calling
• start diploid mapping

Enrichment modules (4:30-5:00)

Extras

• Getting started with Linux and PerlInstalling virtual machines OR samtools tricks OR data formats for UCSC genome browser (DP)
• Linux tutorial (SPHS)

Extras

• RunningUnix & Perl for Biologiststutorial at TACC

Day 2: Calling Genome Variants

• Using the Integrative Genomics Viewer (IGV)
• Shell Scripting
• Mapped read data evaluation (SAMtoolsIntroduction to variant calling (SAMtools) (SPHS - expand to diploid, cover GATK pipeline; annovar seqanswer)
• Assess mapped data (VCF? BAM?) at UCSC genome browser (AW)
• Annotating variants (SPHS/DA)
• Download presentation on Advanced Genome Variant Calling|^Barrick_AdvancedGenomeVariantCalling_2012.pdf||||||||||

Enrichment module (4:30-5:00)

• Installing Linux tools
• Identifying mutations in microbial genomes (breseq)

...

• (JB/)
• Shell Scripting (SPHS/AB)
• Maybe start tophat via script (DA)

Extras

• SRA toolkit, UCSC Genome Browser
• Mapped read data evaluation (SAMtools) (SPHS)
• Calling variants in diploid genomes
• Annotating variants

Additional topics

• Variant calling with GATK
• Genome variation in mixed samples (FreeBayes, deepSNV)
• Identifying structural variants (SVDetect)

...

• Download presentation on Advanced Genome Variant Calling
• Practical advice - short read re-sequencing data

Day 3: RNA-seq

• Intro materials - (SPHS - JB/DA)
• Differential gene expression analysis (JB - bedtools & R)
• Intro materials - splicing (SPHS - JB/DA)
• Differential expression with splice variant analysisTranscriptome assembly & annotation (DA - tophat suite - mention genome ref bundles)
• 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)

• Maybe show how to run tophat here instead of end of day 2?

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 assembliesSRA toolkit, UCSC Genome Browser (bacterial)

Enrichment module (4:30-5:30)

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

Extras

Resources

• Resources : tool list, file formats & more
• Scott's list of linux one-liners
• Example BWA alignment scriptExercises