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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
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 |
Misc
Old Etherpad link: https://etherpad.mozilla.org/g2NxIEAFWL
Day 1: Linux/TACC Introduction
- Linux fundamentals (needs update)
- Getting started at TACC
- Editing files
- Stampede profile Piping and redirection (old)
Misc Day 2: Raw Sequencing data manipulation
- Evaluating raw sequencing dataOverview Example 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 filesOverview of read alignment, references and alignment tools