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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.toc

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

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• 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

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