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
- 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
- Evaluating raw sequencing data
- FASTQC - a good place to start
- FASTX toolkit manipulation of FASTQ data
- Adapter trimming with cutadapt
- 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
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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