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Table of Contents

Your Instructors

  • Anna Battenhouse, Associate Research Scientist, abattenhouse@utexas.edu

    • BA English literature, 1978

    • Commercial software development 1982 – 2007

    • Joined Iyer Lab 2007 (“retirement career”)

    • BS Biochemistry, UT Austin, 2013

    • Joined the Biomedical Research Support Facility (BRCF) and Marcotte Lab summer 2017
    • Also affiliated with
      • Bioinformatics Consulting Group (BCG)
      • Genome Sequencing and Analysis Facility (GSAF)

  • Vy Dang, vyqtdang@utexas.edu

    • Second year graduate student in the Marcotte Lab 

    • Research Interests: Comparative multi-omics, Systems Biology, and Evolution 

  • Riddhiman Garge, riddhimankg@utexas.edu

    • Biochemistry graduate student in the Marcotte Lab

    • Research Interests: Systems Biology, Synthetic Biology, Evolution, Multi-omics

About the Iyer Lab

http://iyerlab.org/

Dr. Vishy Iyer, PI

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Main focus is functional genomics

    • large-scale transciptional reprogramming
      in response to diverse stimuli
    • Encode consortium collaborator
    • work in human and yeast


Research methods include
  • microarrays (Dr. Iyer was co-inventor)

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  • high-throughput sequencing (since 2007)
    • especially ChIP-seq, RNA-seq
    • also miRNA-seq, RIP-seq, MNase-seq ...
    • have ~2,000 NGS datasets

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Communication

Asking questions

...

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Solution
Solution

Solution sections will contain the commands so that you could copy-and-paste them if you have to. They will represent one method of answering the question – but there are often many ways to skin a cat!

Your Instructors

  • Anna Battenhouse, Associate Research Scientist, abattenhouse@utexas.edu

    • BA English literature, 1978

    • Commercial software development 1982 – 2007

    • Joined Iyer Lab 2007 (“retirement career”)

    • BS Biochemistry, UT Austin, 2013

    • Joined the Biomedical Research Support Facility (BRCF) and Marcotte Lab summer 2017
    • Also affiliated with
      • Bioinformatics Consulting Group (BCG)
      • Genome Sequencing and Analysis Facility (GSAF)

  • Vy Dang, vyqtdang@utexas.edu

    • Second year graduate student in the Marcotte Lab 

    • Research Interests: Comparative multi-omics, Systems Biology, and Evolution 

  • Riddhiman Garge, riddhimankg@utexas.edu

    • Biochemistry graduate student in the Marcotte Lab

    • Research Interests: Systems Biology, Synthetic Biology, Evolution, Multi-omics

About the Iyer Lab

...

http://iyerlab.org/

Dr. Vishy Iyer, PI

...

Image Removed

...

Main focus is functional genomics

    • large-scale transciptional reprogramming
      in response to diverse stimuli
    • Encode consortium collaborator
    • work in human and yeast

...

  • microarrays (Dr. Iyer was co-inventor)

...

Image Removed

...

  • high-throughput sequencing (since 2007)
    • especially ChIP-seq, RNA-seq
    • also miRNA-seq, RIP-seq, MNase-seq ...
    • have ~2,000 NGS datasets

...

Course goals

  • Hands-on, tutorial style – learn by doing
    • common bioinformatics tools & file formats
  • Introduce NGS vocabulary
    • both high-level view and practice with specific tools
  • Cover the NGS basics
    • the first few things you'll do after receiving raw sequences
      • raw sequence preparation
      • alignment to reference
      • basic alignment analysis
  • Understand and practice required skills
    • Get you comfortable with Linux and TACC – your best "frenemies"
    • Make you self-sufficient enough in 4 days to become experts over time
    • Show some "best practices" for working with NGS data

...