Page tree
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 27 Next »

This is the home of the Core NGS Tools course, May 2014

This workshop provides an introduction to common analysis tools and file formats currently used in NGS, with emphasis on 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.

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.

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:

Use this to post any questions you have about the lessons and tutorials.

Your Instructors

  • Anna Battenhouse, Associate Research Scientist, Iyer Lab,
  • Dr. Daechan Park, Post-doctoral fellow, Georgio Lab
  • Nathan Abell, Research Assistant, Iyer Lab
  • Amelia Weber Hall, Graduate Student, Iyer Lab


 Info for the instructors

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

ask Scott to add attendees credentials to login8 – Anna

course artifacts – /corral-repl/utexas/BioITeam/core_ngs_tools – make subdirctories & chmod 777 everything

meet 8am Monday


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.

Recently Updated

Navigate space
  • No labels