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

Enrichment modules (4:30-5:00)

• Installing virtual machines OR samtools tricks OR data formats for UCSC genome browser (DP)
• Linux tutorial (SPHS)

Extras

• Running Unix & Perl for Biologists tutorial at TACC

Day 2: Calling Genome Variants

• Introduction 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 (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
• Variant calling with GATK
• Genome variation in mixed samples (FreeBayes, deepSNV)
• Identifying structural variants (SVDetect)
• 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 analysis (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 assemblies (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 script
• Exercises