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 encourage you to use the computers provided in the classroom, but you may also use your personal laptops.
Day 1: Linux and TACC
Day 2: NGS workflow overview and raw sequence pre-processing
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis
Part 1: BEDTools
Part 2: Odds and ends
- Obtaining public datasets from NCBI (needs some revision)
- Visualize mapped data at UCSC genome browser (needs some revision)
- Shell scripting (needs some revision)
meet 7:45 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