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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.

Warning

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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Day 1: Linux/TACC Introduction

Day 2: Raw Sequencing data manipulation

  • Evaluating raw sequencing data
    • Overview of NGS data formats and analyses
    • The FASTA sequencing data format
    • The FASTQ sequencing data format, with Illumina/GSAF-specific details
    • Compression, Linux manipulation of fastq files
    • Overview of sequence quality checking
    • FASTQC - a good place to start
    • FASTX toolkit manipulation of FASTQ data
    • Adapter trimming with cutadapt
    • Batch manipulation of FASTQ files
  • Overview of read alignment, references and alignment tools

Day 3: Alignment and BAM file manipulation

Day 4: Post-Alignment Analysis

Part 1: Bedtools

Part 1: Odds and ends

  • Data formats for visualization (BED, GTF/GFF)
  • UCSC Genome Browser

Enrichment modules

 

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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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 – Amelia

ask Scott to add attendees credentials to login8 – Anna

meet 8am Monday

 

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Tip

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.

Tip
titleRecordings

Contact us for access to recordings of each day's materials after the course is over.

Resources


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