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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (2017_05-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
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- TACC overview
- lecture: the FASTQ format (2017_05-NGSintro.pdf, part 2)
- Working with FASTQ files
- lecture: Sequence QC & preparation (2017_05-NGSintro.pdf, part 3)
- Sequence quality control with FastQC
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- TACC batch jobs
- Trimming sequences
- lecture: Alignment to a reference (2017_05-NGSintro.pdf, part 4)
- Alignment
Day 4: Post-Alignment Analysis
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