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 and TACC
Day 2: Raw Sequencing data manipulation
Day 3: Alignment and BAM file manipulation
Day 4: Post-Alignment Analysis
Part 1: Bedtools
- BED format
- Analysis with bedtools
Part 2: Odds and ends
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
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