Content Comparison

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• 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

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• 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)

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

Extras

Resources

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

Resources tool list, file formats & more