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Core NGS Tools
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  • Day 1: Intro to NGS, Linux and TACC
  • Day 2: TACC batch system and FASTQ files
  • Day 3: Working with raw sequences
  • Day 4: Alignment and BAM file manipulation
  • Day 5: Post-Alignment Analysis
  • Resources
  • Catch up
  • Archive
    • 2023 Core NGS Tools misc
    • 2022 Core NGS Tools Home
    • 2021 Core NGS Tools Home
    • 2020 Core NGS Tools Home
    • Old stuff
      • Alignment (archive)
      • More Alignment exercises 0
      • Copy of good Alignment workflow
      • Samtools: viewing, counting and sorting your alignment data
      • Bedtools: Analyzing your aligned experiment
      • Piping and redirection
      • SAM format and samtools
      • Scott's Linux one-liners
      • Using TACC's Stampede cluster
      • Analysis with bedtools
      • Obtaining public datasets from NCBI
      • Exercise solutions
      • Shell scripting
      • Visualize mapped data at UCSC genome browser
    • Catch-up
    Calendars

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Old stuff

    Old stuff

    May 18, 2018
     Info for the instructors

    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

    Misc Day 1: Linux/TACC Introduction

    • Linux fundamentals (needs update)
    • Piping and redirection (old)

    Misc Day 2: Raw Sequencing data manipulation

    • Example of NGS analyses
    • The FASTA sequencing data format
    • Batch manipulation of FASTQ files


    Old Etherpad link:  https://etherpad.mozilla.org/g2NxIEAFWL
    , multiple selections available,

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