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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 and Raw Sequence structure

Part 1: Linux/TACC Introduction

  • 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

Day 2: Raw Sequencing Quality Evaluation

Part 1: FASTQ manipulation tools

  • Overview of sequence quality checking
  • Evaluating raw sequencing data
  • 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

Day 3: 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

 

 Info for the instructors

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...

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