Page History

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• Anna Battenhouse, Associate Research Scientist, abattenhouse@utexas.edu

  • BA English literature, 1978

  • Commercial software development 1982 – 2007

  • Joined Iyer Lab 2007 (“retirement career”)

  • BS Biochemistry, UT Austin, 2013

  • Joined the Biomedical Research Computing Facility (BRCF) and Marcotte Lab summer 2017
  • Also affiliated with
    • Bioinformatics Consulting Group (BCG)
    • Genome Sequencing and Analysis Facility (GSAF)

• Daryl Barth, daryl.barth@utexas.edu

  • BS Materials Science & Engineering, UC Berkeley, 2017
  • Student Researcher in France and Portugal 2017 - 2018
  • Research Assistant in single cell genomics, UT Southwestern 2019-2021
  • 2nd 3rd year graduate student in the the Marcotte Lab 

  • Research Interests: biomaterials, developmental biology, and bioinformatics

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http://iyerlab.org/ Dr. Vishy Iyer, PI
Main focus is functional genomics large-scale transciptional transcriptional reprogramming in response to diverse stimuli Encode consortium collaborator works in human and yeast
Research methods include microarrays (Dr. Iyer was co-inventor)
high-throughput sequencing (since 2007) especially ChIP-seq, RNA-seq also miRNA-seq, RIP-seq, MNase-seq ... have ~2,000 NGS datasets

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For online attendees, you can also post your question to the Zoom chat. We'll sometimes use breakout rooms when troubleshooting problems you run into. As you login to the Zoom, you'll be assigned to a breakout room where you can join TA Daryl Barth for assistance, if so, TA Daryl Barth will assign you to one.

Getting help

Since most folks are new to the Linux command line, we expect you to run into problems! Please let us know if you're having difficulties!

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We intend this course to offer as much self-learning as possible. Consequently, you'll find many sections like this - click on the triangle to expand them:

and some sections like this:

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• Hands-on, tutorial style – learn by doing
  • common Common bioinformatics tools & file formats
• Introduce NGS vocabulary
  • both high-level view and practice with specific tools
• Cover the NGS basics
  • the The first few things you'll do after receiving raw sequences
    
    • raw sequence QC and preparation
    • alignment to reference
    • basic alignment analysis
• Understand and practice required skills
  • Get you comfortable with Linux and TACC – your best "frenemies"
  • Make you self-sufficient enough in 5 days to become experts over time
  • Show some "best practices" for working with NGS data

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Analysis – making sense of raw data one part bioinformatics and statistics one part scripting / programming Linux command line High Performance Computing (TACC) bash scripting (grep, awk, sed) R, python, perl Management – making order out of chaos one part organization one part data wrangling Adoption of best practices is critical!

Large and growing datasets

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• yeast:  5 – 20 million reads
• human:  20 – 250 million reads (~5 - 8 million for TagSeq)
• single end (SE) or paired end (PE), length 75 50 – 250 bases300 bases (100 or 150 typical)

The initial fastq FASTQ files are big (100s of MB to GB) – and they're just the start.

• Organization and naming conventions are critical.
• Your data can get out of hand very quickly!

progression Progression of Iyer Lab datasets over time:

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