Page History

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Day 1: Linux/TACC Introduction and Raw Sequence structure

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• Linux

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• Linux Fundamentals
  • Getting started
  • Editing files
  • Stampede profile
  • Piping and redirection

Part 2: TACC introduction

• Using TACC's Stampede cluster
  • Stampede file systems

Day 2: Raw Sequencing Quality Evaluation

Part 1: FASTQ manipulation tools

• Overview of NGS data formats and analyses
• The FASTA sequencing data format
• The FASTQ sequencing data format, with Illumina/GSAF-specific details
• Compression, Linux manipulation of fastq files
• Overview of sequence quality checking
• Evaluating raw sequencing data
• 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

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