Content Comparison

Communication

Post its

Green post-it – I'm good at the moment.

Pink post-it – I need a bit of help.

Conventions

If you see a block of text like this:

ls -h

it means, type the command ls -h into a terminal window, hit return, and see what happens.

We intend this course to offer as much self-learning as possible. Consequently, you'll find many sections like this - click on the triangle to expand them:

and some sections like this:

Your Instructors

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

  • BA English literature, 1978

  • Commercial software development 1982 – 2005

  • Joined Iyer Lab 2007 (“retirement career”)

  • BS Biochemistry, UT Austin, 2013

  • Joined Marcotte lab and Biomedical Research Support Facility (BRCF) in summer 2017

• Haridha Shivram, haridh@utexas.edu

  • 6th year graduate student in the Iyer Lab

• Claire McWhite, claire.mcwhite@utexas.edu

  • 5th year graduate student in the Marcotte Lab

...

http://iyerlab.org/ Dr. Vishy Iyer, PI
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)
high-throughput sequencing (since 2007) especially ChIP-seq also RNA-seq, RIP-seq, MNase-seq ... we now have nearly 2,000 NGS datasets

Communication

Post its

Green post-it – I'm good at the moment.

Pink post-it – I need a bit of help.

Conventions

If you see a block of text like this:

ls -h

it means, type the command ls -h into a terminal window, hit return, and see what happens.

We intend this course to offer as much self-learning as possible. Consequently, you'll find many sections like this - click on the triangle to expand them:

...

Hint sections will provide you some guidance on what to do next, but will not spell it out.

and some sections like this:

...

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

...