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
- Alignment (NA)
Part 2: SAM/BAM format and manipulation
- The SAM file format specification
- Manipulating BAM files with samtools
- Alignment filtering examples
Day 4: Post-Alignment Analysis
Part 1: Bedtools
Part 1: Odds and ends
- Data formats for visualization (BED, GTF/GFF)
- UCSC Genome Browser
Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL
Use this to post any questions you have about the lessons and tutorials.
- Anna Battenhouse, Associate Research Scientist, Iyer Lab, email@example.com
- Dr. Daechan Park, Post-doctoral fellow, Georgio Lab
- Nathan Abell, Research Assistant, Iyer Lab
- Amelia Weber Hall, Graduate Student, Iyer Lab
name tags & sign in sheets?
visit room to check out video hookups, lab computers
print cheat sheets
obtain allocation info from Hans
ask Scott to add attendees credentials to login8
meet 8am Monday
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