May 2013

We will meet in Room 101B of the Flawn Academic Center (FAC) building. We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops.

1 May 2013
- 1.1 Your Instructors
- 1.2 Day 1: Linux/TACC Introduction and Read Mapping
  - 1.2.1 Part 1: Linux/TACC Introduction
  - 1.2.2 Part 2: Read Mapping
    - 1.2.2.1 Enrichment modules (4:30-5:30)
    - 1.2.2.2 Extras
- 1.3 Day 2: Handling Raw and Aligned sequences, and Calling Genome Variants
  - 1.3.1 Part 1. Handling Raw and Aligned sequences
  - 1.3.2 Part 2. Calling Genome Variants
    - 1.3.2.1 Enrichment module (12:30-1:30)
    - 1.3.2.2 Enrichment modules (4:30-5:30)
    - 1.3.2.3 Extras
- 1.4 Day 3: RNA-seq
  - 1.4.1 Part 1. Introduction to RNA-seq Counting
  - 1.4.2 Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)
    - 1.4.2.1 Enrichment module (12:30-1:30)
    - 1.4.2.2 Enrichment modules (4:30-5:30)
    - 1.4.2.3 Extras
- 1.5 Day 4: Assembly and Annotation
  - 1.5.1 Part 1. Genome Assembly
  - 1.5.2 Part 2. Assembly Annotation
    - 1.5.2.1 Enrichment module (12:30-1:30)
    - 1.5.2.2 Enrichment module (4:30-5:30)
- 1.6 Resources

Resources tool list, file formats & more

Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL

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

Your Instructors

Name	Initials	Affiliation	Expertise

Name	Initials	Affiliation	Expertise
Scott Hunicke-Smith	SPHS	Director GSAF	Everything, if loosely defined (but especially `awk`)
Jeff Barrick	JB	Asst. Prof. Biochemistry	Microbes, Perl, C++, Mac, miscellanea
Dhivya Arasappan (in absentia)	DA	GSAF	RNA-seq, transcriptome assembly
Anna Battenhouse	AB	Iyer Lab	Eukaryotes, Bash scripting, UCSC Genome Browser
Daechan Park	DP	Iyer Lab	Eukaryotes, ChIP-seq, Python, Samtools
Nichole Bennett	NB	Parmesan/Singer Labs	Python, R, Unix
Dan Deatherage	DD	Barrick Lab	Unix, Python, NGS Library Prep
Nathan Abell	NA	Iyer Lab	Eukaryotes, RNA-Seq

instructor action item list

Day 1a: Scott 1b: Jeff
Day 2a: Jeff, Daechan, Anna, 2b: Scott
Day 3a: Jeff 3b: Iyer lab
Day 4a: Jeff, 4b: Scott

Instructors: meet 9am Monday for final check

Each Part 1/Part 2 section needs to be standardized with:
*Learning Objectives
*Theory
*Workflow diagram (data, toolbox/recipe, exercises)
*Tutorial (bulk of time here)
*Recap learning objectives
*Next steps...

Day 1: Linux/TACC Introduction and Read Mapping

Part 1: Linux/TACC Introduction

Part 2: Read Mapping

Introduction to next-gen sequencing technologies (JB)
Variant calling workflow diagram:
(JB)
Mapping tutorial (bowtie, BWA, bowtie2) (JB)

Enrichment modules (4:30-5:30)

Sharing Linux tricks - linux one-liners (SPHS)
Working on TACC from your Mac or PC (AB)
- Editing files, more detail

SSC Intro to NGS Bioinformatics Course

May 2013

Your Instructors

Day 1: Linux/TACC Introduction and Read Mapping

Part 1: Linux/TACC Introduction

Part 2: Read Mapping

Enrichment modules (4:30-5:30)

Extras

Day 2: Handling Raw and Aligned sequences, and Calling Genome Variants

Part 1. Handling Raw and Aligned sequences