2021-04-26-umich-rnaseqDemystified

Welcome to RNA-Seq Demystified

About this workshop

• By the end of the workshop, attendees will be able to

  • Transform raw sequencing data into annotated differential expression values using a suite of open-source tools.
  • Identify common data quality problems and understand their impact and possible mitigations
  • Visualize differential expression data in RStudio plots.

• This workshop is targeted toward researchers who would like to be able to run RNA-Seq analysis on their own. It assumes a very basic familiarity with genetics, the command line, and R or R-Studio.

• Our purpose is not to be exhaustive, and we don't expect anyone to be an expert at the end of the workshop. But we hope you will have a familiarity with key concepts, data types, tools, and how they all connect to one another in the service of a biological question.

• The first day will be a mix of hands-on content and lecture-style components, while the second day will primarily be a hands-on experience.

• Please let us know if there is anything we can do to improve the workshop experience.

Thanks to our sponsors

• Biomedical Research Core Facilities

  Biomedical Research Core Facilities (BRCF) helps researchers economically take advantage of the latest technology and collaborate with top experts in the field. Established in 1986, the BRCF was formed to offer centralized access to research services and equipment.

• University of Michigan Library

  Our mission is to support, enhance, and collaborate in the instructional, research, and service activities of faculty, students, and staff, and contribute to the common good by collecting, organizing, preserving, communicating, sharing, and creating the record of human knowledge.

• Michigan Institute for Data Science (MIDAS)

  To strengthen University of Michigan’s preeminence in Data Science and to catalyze the transformative use of Data Science in a wide range of disciplines to achieve lasting societal impact.

What is the Bioinformatics Core?

• The UM Bioinformatics Core is a team seven analysts; we help researchers design, analyze, and interpret high-throughput genomics experiments.
• Last year we helped about 60 researchers design and execute about 100 projects across:
  • gene expression
  • variant calling, copy-number analysis
  • chromatin accessibility and binding
  • DNA methylation
  • single-cell experiments
  • custom bioinformatic analyses
• We provide letters of support for grant proposals.
• We are also creating a series of bioinformatics-focused workshops

Who are your hosts/instructors?

• Chris Gates cgates@umich.edu
• Marci Brandenburg mbradenb@umich.edu
• Dana King damki@umich.edu
• Travis Saari trsaari@umich.edu
• Helpers

Housekeeping

Code of Conduct (CoC)

• Be kind to others. Do not insult or put down others. Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate for the workshop.

• All communication should be appropriate for a professional audience including people of many different backgrounds. Sexual language and imagery is not appropriate.

• The Bioinformatics Core is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion. We do not tolerate harassment of participants in any form.

• Thank you for helping make this a welcoming, friendly community for all.

• If you have questions about the CoC please reach out to the hosts during the workshop, or email us at bioinformatics-workshops@umich.edu.

• To report a CoC incident/concern, please email Chris Gates (Bioinformatics Core, Managing Director) at cgates@umich.edu or contact the University of Michigan Office of Institutional Equity at institutional.equity@umich.edu.

Workshop patterns and Zoom controls

• We will be recording this session. Recordings will be available to participants following the workshop.

• Zoom controls are at the bottom of the Zoom window:

• To minimize distractions, we encourage participants to keep their audio muted (1) (unless actively asking a question).

• To maximize engagement, we encourage participants to keep their video on.

• Chat can be used to communicate to the group or to individuals.

• Zoom's "non-verbal controls" are a useful way to interact

  • Depending on your version of Zoom you can access these either
    • in the Reactions button on you main Zoom window
    • at the bottom of the Participant pane

• Raise Hand to request clarification or ask a question. (Same an in-person workshop.)
• Yes when you complete an assigned task or other instructor feedback
• No to request assistance from helper
  • Hosts will connect you with a helper in a breakout room.

Schedule

Time	Topic	Instructor
Day 1
9:00	Workshop Introduction	Chris Gates
9:15	Warming Up, Quality Control	Travis Saari
10:30	Break
	Reference Genomes, Alignment, Quantification, QC
1:00	Day 1 concludes
Day 2
9:00	Intro Day 2	Chris Gates
9:10	Introduction to DESeq2, Count Normalizations, Models	Dana King
10:30	Break
	Comparisons, Annotations, Visualization
12:45	Wrap-up	Chris Gates
1:00	Workshop concludes

Any questions?

Breakout Rooms

• We're all going to be transported into randomized breakout rooms to see what that's like.
• Introduce yourself and share a reason you signed up for this workshop.
• When you have completed introductions, you can leave the breakout room to rejoin the main room.

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*The workshop Code of Conduct has been adapted the NumFocus Code of Conduct (https://numfocus.org/code-of-conduct) which itself draws frin from numerous sources, including the Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license, the Contributor Covenant version 1.2.0, the Bokeh Code of Conduct, the SciPy Code of Conduct, the Carpentries Code of Conduct, and the NeurIPS Code of Conduct.

This workshop content is licensed under a Creative Commons Attribution 4 License.

Sections of the workshop content have been adapted and extended from materials created by the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.