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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

Linux Fundamentals

Using TACC's Stampede cluster
- Stampede file systems

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

Alignment (NA)
SAM format and samtools

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

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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