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.

...

Day 1: Intro to NGS,

...

Linux and TACC

• Introduction
• Getting started at TACC – logging in

Day 2: Raw Sequencing data manipulation

Day 3: Alignment and BAM file manipulation

• Alignment  (NA)
• SAM format and samtools

Day 4: Post-Alignment Analysis

Part 1: BEDTools

• Analysis with bedtools
• Analysis with BEDTool

Part 2: Odds and ends

• Visualize mapped data at UCSC genome browser
• Obtaining public datasets from NCBI
• Shell scripting

Core NGS Tools -- Resources

...

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

add attendees credentials to login8 – Anna

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

meet 8am Monday

web URL: http://loving.corral.tacc.utexas.edu/bioiteam/

• 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: Alignment and BAM file manipulation

• 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

• Filtering with SAMTools
• Analysis using BEDTools

Resources

• Linux fundamentals

• Core NGS Resources

• Decimal and Hexadecimal
• Data wrangling best practices
• Catch-up

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.