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This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91282159612. Please make sure your version of Zoom is at least 5.0 (see https://zoom.its.utexas.edu/zoom-upgrade). There will be a short break each day around 10:30am. |
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Contact us for access to recordings of each day's materials. |
Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (2020_06-NGSintro.pdf, part 1)
- Setting up your TACC environmentRecording of
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Day 2: Transferring files and TACC
- File systems and transferring files
- lecture: NGS Terminology (2020_06-NGSintro.pdf, part 2)
- TACC batch jobsRecording of
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Day 3: Working with raw sequences
- lecture: the FASTQ format (2020_06-NGSintro.pdf, part 3)
- Working with FASTQ files
- lecture: Sequence QC & preparation (2020_06-NGSintro.pdf, part 3)
- Sequence quality control
- TrimmingRecording of
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Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
- The Alignment workflow – references
- lecture: Alignment to a reference (2020_06-NGSintro.pdf, part 4)
- The Alignment workflow – performing an alignmentRecording of Day 4 (with audio transcript)https://utexas.zoom.us/rec/share/tetwPp_Z9TlLT9bC133DcZYcBJXeaaa8hyYaq6BeyUm3-JyDAmfZnmavTCHggXXm
Day 5: Post-Alignment Analysis
- Filtering with SAMTools
- Analysis using BEDToolsRecording of Day 5 (with audio transcript)https://utexas.zoom.us/rec/share/28Mpdrrcyj1LGY2Oq3vVQLQaGNjIeaa8hycaqPsPmh19xM2h0kUCr0GY-taXU2Th
Resources
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