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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.

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





Scott Hunicke-Smith


Director GSAF

Everything, if loosely defined (but especially awk)

Jeff Barrick


Asst. Prof. Biochemistry

Microbes, Perl, C++, Mac, miscellanea

Dhivya Arasappan (in absentia)



RNA-seq, transcriptome assembly

Anna Battenhouse


Iyer Lab

Eukaryotes, Bash scripting, UCSC Genome Browser

Daechan Park


Iyer Lab

Eukaryotes, ChIP-seq, Python, Samtools

Nichole Bennett


Parmesan/Singer Labs

Python, R, Unix

Dan Deatherage


Barrick Lab

Unix, Python, NGS Library Prep

Nathan Abell


Iyer Lab

Eukaryotes, RNA-Seq

instructor action item list

 Info for the instructors

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
*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

Enrichment modules (4:30-5:30)


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

Part 1. Handling Raw and Aligned sequences

Part 2. Calling Genome Variants

Enrichment module (12:30-1:30)

Enrichment modules (4:30-5:30)


Day 3: RNA-seq

Part 1. Introduction to RNA-seq Counting

Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)

Enrichment module (12:30-1:30)

Enrichment modules (4:30-5:30)


Day 4: Assembly and Annotation

Part 1. Genome Assembly

Part 2. Assembly Annotation

Enrichment module (12:30-1:30)

  • Office hours: "I want to learn how to install and use this tool called ______ that we didn't talk about in class." (JB).

Enrichment module (4:30-5:30)


As you're getting settled

  • No labels
Page: Lonestar Profile Page: Diagram of Lonestar's directories Page: Diagram of running a job on Lonestar Page: Evaluating your raw sequencing data Page: Mapping tutorial Page: Integrative Genomics Viewer (IGV) tutorial Page: Workflow diagram of variant calling Page: Getting started with Unix and Perl Page: Variant calling tutorial Page: Visualize mapped data at UCSC genome browser Page: Annotating Variants Page: Installing Linux tools Page: Shell Script Page: Mapped read data evaluation (SAMtools) Page: Calling variants in diploid or multiploid genomes Page: Variant calling with GATK Page: Genome variation in mixed samples (FreeBayes, deepSNV) Page: Identifying structural variants (SVDetect) Page: Practical advice - short read re-sequencing data Page: SRA toolkit Page: Differential gene expression analysis Page: Differential expression with splice variant analysis aug2012 Page: Identifying mutations in microbial genomes (breseq) Page: non-coding RNA analysis Page: Genome Assembly Page: Genome Assembly (velvet) Page: Genome Annotation (Glimmer3) Page: Evaluating & Visualizing assemblies Page: Custom Genome Databases Page: Transcriptome assembly & annotation Page: Scott's list of linux one-liners Page: Exercises Page: Introduction to genome variation Page: instructor action item list Page: General introduction Page: Recap and "for further study" Page: Handling Sequences Overview Page: As you're getting settled Page: Editing files Page: Installing Linux virtual machine on Windows Page: Installing Virtual machine & Linux on Windows Page: Key take home points Page: Linux final Page: Linux start Page: Samtools tricks Page: Start tophat by submitting to lonestar Page: Tutorial - Start diploid mapping for Day 2 Page: Using SFTP for file browsing on Linux.