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This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91282159612.91965141761 There will be a short break each day around 10:30am. Your TACC account will remain on our class' TACC project allocation through June 30, 2021. |
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Contact us for access to recordings of each day's materials after the course is over. |
Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (20202021_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2:
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TACC batch system and FASTQ files
- lecture: NGS Terminology ( 2020
- 2021_06-NGSintro.pdf, part 2)
- TACC batch jobs
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- lecture: the FASTQ format (20202021_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation ( 2020
- 2021_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference ( 2020
- 2021_06-NGSintro.pdf, part 4)
- The Basic Alignment workflow – referencesWorkflow
- lecture: Alignment to a reference ( 2020
- 2021_06-NGSintro.pdf, part 4)
- The Alignment workflow – performing an alignmentMore Alignment exercises
Day 5: Post-Alignment Analysis
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