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 STRONGLY encourage you to use the computers provided in the classroom, but you may also bring 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, 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
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Day 1: Linux/TACC Introduction and Raw Sequence structure
Part 1: Linux/TACC Introduction
- Overview of NGS data analysis
- Linux Fundamentals
- Overview of the TACC Stampede cluster
- Transferring files to/from TACC
Part 2: Sequencing formats
- The FASTA sequencing data format
- The FASTQ sequencing data format, with Illumina/GSAF-specific details
- Compression, Linux manipulation of fastq files
Day 2: Raw Sequencing Quality Evaluation
Part 1: FASTQ manipulation tools
- Overview of sequence quality checking
- FASTQC - a good place to start
- FASTX toolkit manipulation of FASTQ data
- Adapter trimming with cutadapt
Part 2: FASTQ manipulation at TACC
- Running batch jobs at TACC
- Batch manipulation of FASTQ files
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: Alignment and BAM file manipulation
Part 1: Alignment and aligners
- Overview of read alignment, references and alignment tools
- BWA overview, relevant options
- Bowtie2 overview, relevant options
Part 2: SAM/BAM format and manipulation
- The SAM file format specification
- Manipulating BAM files with samtools
- Alignment filtering examples
Day 4: Post-Alignment Visualization and Analysis
Part 1: Visualization tools and formats
- Data formats for visualization (BED, GTF/GFF)
- The Integrative Genomics Viewer (IGV)
- UCSC Genome Browser
Part 2: SAM/BAM format and manipulation
- Analysis with bedtools – intersect, coverage, merge
- Obtaining public datasets from GEO
- Other NGS tools and resources
Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL
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
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Instructors: meet 8am Monday
Each Part 1/Part 2 section needs to be standardized with:
*Learning Objectives
*Theory
*Workflow diagram (data, toolbox/recipe, exercises)
*Tutorial (bulk of time here)
*Recap learning objectives
*Next steps...
- 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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