This is the home of the Core NGS Tools space, May 2014
We will meet in Room 101B of the Flawn Academic Center (FAC) building. We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops.
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course, June 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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This workshop will be held via Zoom, URL |
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Use this to post any questions you have about the lessons and tutorials.
Your Instructors
- Anna Battenhouse, Associate Research Scientist, Iyer Lab, abattenhouse@utexas.edu
- Dr. Daechan Park, Post-doctoral fellow, Georgio Lab
- Nathan Abell, Research Assistant, Iyer Lab
- Amelia Weber Hall, Graduate Student, Iyer Lab
Macros This page includes some basic macros. As you create pages, add news items and comments, you'll see the macros below fill up with all the activity in your space. Macros are your friends: look for the Macro icon in the Rich Text editor options when you're editing a page.
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 (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: Post-Alignment Analysis
Resources
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