Introduction

Your Instructors

We are members (or alumni) of the functional genomics lab of Vishwanath Iyer, UT Austin.

Anna Battenhouse, Associate Research Scientist, Iyer Lab, abattenhouse@utexas.edu
Dr. Daechan Park, Post-doctoral fellow, Georgiou Lab, daechan.park@utexas.edu
Nathan Abell, Research Assistant, Iyer Lab, abell.nathan@gmail.com
Amelia Weber Hall, Graduate Student, Iyer Lab, ameliahall@utexas.edu

Goals

Hands-on, tutorial style – learn by doing
Cover the NGS tool basics – the first few things you'll do after receiving raw sequences
Get you comfortable with Linux and TACC – your best "frenemies"
Make you self sufficient in 4 days to become experts over time
Show some "best practices" for working with NGS data

Communication

Post its

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

Pink post-it – I need a bit of help.

Etherpad

Link to Etherpad: https://etherpad.mozilla.org/yUFlDtWv2c

Use this to post any questions you have about the lessons and tutorials.

Conventions

Text that you find in courier font refers to a program or file name on a computer.

If you see a block of text like this:

Example code block

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

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

and some sections like this:

Solution

Solution sections will contain the commands so that you could copy-and-paste them if you have to. They should be exactly accurate.

About the Iyer Lab

http://iyerlab.org/

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
  - http://lad.icmb.utexas.edu

- high-throughput sequencing (since 2007)
  - especially ChIP-seq
  - also RNA-seq, RIP-seq, MNase-seq ...
  - we now have > 1,200 NGS datasets

Anna's background
- BA English literature, 1978
- Commercial software development 1982 – 2005
- Joined Iyer Lab 2007 (“retirement career”)
- BS Biochemistry, 2013
Daechan's background
- BS Biology, Seoul National University, 2008
- Ph.D Cell and Molecular Biology, UT Austin, 2014
- Baby sitting, Current

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