This is the home of the Core NGS Tools space, May 2014

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.

Day 1: Linux/TACC Introduction and Raw Sequence structure

Part 1: Linux/TACC Introduction

• Overview of NGS data analysis
• Linux fundamentals, general practice
• Overview of the TACC Stampede cluster
• Transferring files to/from TACC

Part 2: Sequencing formats

• The FASTA sequencing data format
• The FASTQ sequencing data format, with Illumina/GSAF-specific details
• Compression, Linux manipulation of fastq files

Day 2: Raw Sequencing Quality Evaluation

Part 1: FASTQ manipulation tools

• Overview of sequence quality checking
• FASTQC - a good place to start
• FASTX toolkit manipulation of FASTQ data
• Adapter trimming with cutadapt

Part 2: FASTQ manipulation at TACC

• Running batch jobs at TACC
• Batch manipulation of FASTQ files

Day 3: Alignment and BAM file manipulation

Part 1: Alignment and aligners

• Overview of read alignment, references and alignment tools
• BWA overview, relevant options
• Bowtie2 overview, relevant options
• Adapter trimming with cutadapt

Part 2: FASTQ manipulation at TACC

• Running batch jobs at TACC
• Batch manipulation of FASTQ files

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

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

Your Instructors

• Anna Battenhouse, Associate Research Scientist, Iyer Lab, abattenhouse@utexas.edu
• Dr. Daechan Park, Post-doctoral fellow, Georgio Lab
• Nathan Abell, Research Assistant, Iyer Lab
• Amelia Weber Hall, Graduate Student, Iyer Lab

Macros This page includes some basic macros. As you create pages, add news items and comments, you'll see the macros below fill up with all the activity in your space. Macros are your friends: look for the Macro icon in the Rich Text editor options when you're editing a page.

Navigate space