Page Comparison

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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 Support Facility (BRCF) and Marcotte Lab summer 2017
  • Also affiliated with
    • Bioinformatics Consulting Group (BCG)
    • Genome Sequencing and Analysis Facility (GSAF)

• Rachael Cox, rachaelcox@utexasDaryl Barth, daryl.barth@utexas.edu

  • BS Organic Chemistry, 2013
  • Junior R&D chemist 2014-2018
  • Started PhD in Biochemistry in 2018
  • Third ??
  • ?? year graduate student in the Marcotte Lab 

  • Research Interests: Comparative multi-omics, systems biology, and protein complex evolution??

About the Iyer Lab (where Anna learned NGS)

http://iyerlab.org/ Dr. Vishy Iyer, PI
Main focus is functional genomics large-scale transciptional reprogramming in response to diverse stimuli Encode consortium collaborator work 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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Feel free to ask questions any time during the instructor's lecture and demonstrations.

You For online attendees, you can also post your question to the Zoom chat.

Breakout rooms

We'll sometimes use breakout rooms when working on short assignments, and when troubleshooting problems you run into. As you login to the Zoom, you'll be assigned to a breakout rooms where you can join TA Rachael Cox Daryl Barth for assistance.

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 in the Zoom chat. !

Making mistakes and running into problems is key to learning the Linux command line! It is not only expected – it is encouraged . So once you tell us you're having an issue and get our attention, we encourage you to share your screen so everyone can benefit from shared troubleshooting.If you'd prefer not to share your screen with with the class, the TA may ask you to join a breakout room to help you, depending on the issue.

Conventions

If you see a block of text like this:

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it means, type the command ls -h into a terminal window, hit Enter, and see what happens.

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:

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• yeast:  5 – 20 million reads
• human:  20 – 250 million reads (~5 - 8 million for TagSeq)
• single or paired end, length 75 – 250 bases

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