This is the home of the Core NGS Tools course, May 2014June 2021, 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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This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/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,
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Linux and TACC
Day 2: Raw Sequencing data manipulation
Day 3: Alignment and BAM file manipulation
- – logging in
- lecture: NGS overview & technology (2021_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
Day 2: TACC batch system and FASTQ files
- lecture: NGS Terminology (2021_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (2021_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation (2021_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- lecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4)
- More Alignment exercises
Day 5
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: Post-Alignment Analysis
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Part 2: Odds and ends
Resources
- Linux fundamentals
- Obtaining public datasets from NCBI
- Visualize mapped data at UCSC genome browser
- Shell scripting
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room key – should be automatically opened at 7:30 am name tags – Rayna will provide sign in sheet & sign to room – Amelia visit room to check out video hookups, lab computers – Rayna will give us time print cheat sheets – Amelia obtain allocation info from Hans – Anna add attendees credentials to login8 – Anna course artifacts – /corral-repl/utexas/BioITeam/core_ngs_tools – make subdirctories & chmod 777 everything meet 8am Monday web URL: http://web.corral.tacc.utexas.edu/BioITeam
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