This is the home of the Core NGS Tools course, May 2014June 2023, at https://wikis.utexas.edu/display/CoreNGSTools
This workshop provides an introduction to common analysis tools and file formats currently used in NGS, with emphasis on quality assessment and manipulation of raw NGS sequences (FastQC, cutadapt), read mapping (bwa, bowtie2), the Sequence Alignment Map (SAM) format, and tools for manipulating BAM files (samtools, bedtools). Participants will gain hands-on experience using these and other NGS tools in the Linux command line environment at TACC, as well as exposure to the many bioinformatics resources TACC makes available.
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We will meet in Room 101B of the Flawn Academic Center (FAC) building. We encourage you to use the computers provided in the classroom, but you may also use your personal laptops. |
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Day 1: Intro to NGS,
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Linux and TACC
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- – logging in
- lecture: NGS
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- overview & technology (2023_06-NGSintro.pdf part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2: TACC batch system and FASTQ files
- Catch up day 1 TACC setup
- lecture: NGS Terminology (2023_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (2023_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation (2023_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2023_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- lecture: Alignment to a reference (2023_06-NGSintro.pdf, part 4)
- More Alignment exercises
Day 5: Post-Alignment Analysis
Resources
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- Overview NGS data processing
- Pre-processing FASTQ sequences
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis
- Analysis using BEDTools
- Odds and ends
Core NGS Tools -- Resources
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meet 8 am Monday – students will start ariving ~8:30. room key – should be automatically opened at 7:30 am name tags – Rayna will provide; pick up from her Friday at Big Data sign in sheet & sign to room – Amelia visit room to check out video hookups, lab computers – Friday 12:45 - 1pm
print cheat sheets – Amelia obtain stampede allocation info from Hans – Anna add attendees credentials to stampede login8 – Anna course artifacts – /corral-repl/utexas/BioITeam/core_ngs_tools – make subdirctories & chmod 777 everything web URL: http://web.corral.tacc.utexas.edu/BioITeam, corresponds to /corral-repl/utexas/BioITeam/web
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