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DaveClements/UCDavis2013ShortCourse

UC Davis Genome Center

UC Davis 2013 Bioinformatics Short Course

Resource

UC Davis 2013 Short Course

Types
Tutorials, Datasets, VM, AMI
Domains

Everything (almost)

Owners

Joe Fass <jnfass AT ucdavis DOT edu>, Nikhil Joshi <najoshi AT ucdavis DOT edu>, Jessie Li <jjsli AT ucdavis DOT edu>, Monica Britton <mtbritton AT ucdavis DOT edu>, Blythe Durbin-Johnson <bpdurbin AT phs DOT ucdavis DOT edu>

Formats
Slides, Web Pages, Documents
Date Created/Updated
2013/09

These materials are from a week-long workshop offered at UC Davis in September 2013. They include slides, hands=-in exercises, sample datasets, and even and AMI and VM image.

Outline

The entire course is available online:

Monday

  • 2013 Bioinformatics Short Course - Welcome Lecture
  • Next Generation Sequencing Fundamentals - lecture
  • Read Quality Assessment & Improvement - lecture

  • Introduction to Galaxy and Sequence Quality Assessment & Improvement - exercises

  • Running Workflows - exercises
  • Creating Workflows from scratch - exercises

Tuesday

  • Next Generation Sequence Alignment - lecture
  • Next Generation Sequence Alignment - exercises
  • GATK Best Practices for Variant Discovery - lecture
  • Variant Discovery exercise
  • Effect Prediction and the UCSC Genome Browser
  • Useful links for GATK variant analysis and snpEff

Wednesday

  • Genome Assembly - lecture
  • Genome Assembly - exercises
  • Assembly Assessment, and the Assemblathon Competitions - lecture

Thursday

  • RNA-Seq Concepts, Terminology, and Work Flows - lecture
  • Aligning SE RNA-Seq Reads to a Reference Genome - exercises
  • RNA-Seq Statistics - lecture
  • Aligning PE RNA-Seq Reads to a Genome - exercises
  • Gene Construction - lecture and exercises
  • Alignment to a Reference Transcriptome - exercises
  • Transcriptome Assembly - mini-lecture
  • Some Helpful Links

Friday

  • Friday Lectures & Panel Discussion

  • Amazon Cloud Computing
  • Unix Command Line bootcamp
  • Command Line RNA-Seq

CategoryTrainingResource