Wrapping up

We hope you now have more familiarity with key concepts, data types, tools, and how they all connect to enable gene expression analysis from bulk RNA-Seq data.


Housekeeping


Looking ahead

Workshop environment

  • BASH/RStudio workshop compute environment will be available until 3/31.

    • Please save all your R scripts now so that we can “right-size” the compute environment immediately following today’s workshop session.
  • You can download files from the workshop environment from your terminal/command line window as below. (You will need to substitute your actual workshop username and type workshop password when prompted.)

    mkdir rnaseq-demystified-workshop
    cd rnaseq-demystified-workshop
    scp -r YOUR_USERNAME@bfx-workshop01.med.umich.edu:"RSD*" .
    • Note that the full download is about 2-4Gb, so depending on your internet speeds it could take while.

Installing software locally

  • You can install necessary programs to run programs locally. Note that for typical data, the compute intensive steps (Day 1) assume your computer has powerful compute (many CPUs and lots of RAM) and sizable storage capacity. (i.e. It may not be practical to run these on your laptop.)
  • Installing bioinformatics software is non-trivial and comprehensive instructions to setup a complete compute environment are outside the scope of this workshop. (We are considering offering a Computational Reproducibility workshop that would cover this.) For the intrepid, see relevant links below:

University of Michigan Resources

  • UM CoderSpaces “office hours” and UM CoderSpaces Slack workspace. (See “Useful Resources” section in above page for instructions on how to join and access the CoderSpaces Slack workspace.)
  • Upcoming UM Advanced Research Computing workshops.
  • Advanced Research Computing (ARC) at University of Michigan hosts a high-performance computing (HPC) platform called Great Lakes which combines high-end computers, fast/resilient storage, and pre-installed software. GreatLakes may be a good resource for folks who need to run the more compute intensive steps and a substantial block of compute and storage is subsidized by ARC making it essentially free to many researchers.

Training and support


Thank you

Sponsors

Thank you to/from the workshop team

Chris Marci Travis Dana
Raymond Nick Weisheng


Thank you for participating in our workshop. We welcome your questions and feedback now and in the future.

Bioinformatics Workshop Team

bioinformatics-workshops@umich.edu
https://brcf.medicine.umich.edu/bioinformatics