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.
We will meet in Room 101B of the Flawn Academic Center (FAC) building. We encourage you to use the computers provided in the classroom, but you may also use your personal laptops.
This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91965141761
There will be a short break each day around 10:30am.
Your TACC account will remain on our class' TACC project allocation through June 30, 2021.
Contact us for access to recordings of each day's materials after the course is over.
Day 1: Intro to NGS, Linux and TACC
Day 2: NGS workflow overview and raw sequence pre-processing
- Overview NGS data processing
- Pre-processing FASTQ sequences
Day 2: TACC batch system and FASTQ files
Day 3: Working with raw sequences
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4)
- lecture: Alignment
- SAM format and samtools
- to a reference (2021_06-NGSintro.pdf, part 4)
Day 5: Post-Alignment Analysis
- Filtering with SAMTools
- Analysis using BEDToolsOdds and ends
- Obtaining public datasets from NCBI
- Visualize mapped data at UCSC genome browser Shell scripting
meet 8 am Monday – students will start ariving ~8:30.
room key – should be automatically opened at 7:30 am
name tags – Rayna will provide; pick up from her Friday at Big Data
sign in sheet & sign to room – Amelia
visit room to check out video hookups, lab computers – Friday 12:45 - 1pm
- last year all the classroom computers used credentials userid: student password: hookem
- check whether this is still true or if UT EIDs are required
print cheat sheets – Amelia
obtain stampede allocation info from Hans – Anna
add attendees credentials to stampede login8 – Anna
course artifacts – /corral-repl/utexas/BioITeam/core_ngs_tools – make subdirctories & chmod 777 everything
web URL: http://web.corral.tacc.utexas.edu/BioITeam, corresponds to /corral-repl/utexas/BioITeam/web