University of Alabama at Birmingham
July 09-10, 2024
8:00am - 5:00 pm CST
Instructors: Austyn Trull, Bharat Mishra, Lara Ianov, Luke Potter, and Nilesh Kumar
Helpers: Gurpreet Kaur, Kristen Coutinho, Samuel Bharti, Shaurita Hutchins, and Tarun Mamidi
Register now at this link
This event is a two-day example-driven hands-on workshop designed to teach introductory Bulk RNA Seq. The workshop will cover the following topics:
Introduction to raw data management and data exploration.
Secondary analysis with nf-core/rnaseq.
Tertiary analysis including quality control, data normalization, gene annotation, gene enrichment analysis.
Fundamentals of data visualization for transcriptomics and data interpretation.
This workshop is designed as a foundation upon which more specialized skills can be built, but will not delve into transcriptomics beyond bulk RNA-seq or other advanced topics in computational biology or software development. These topics will be covered in later workshops.
Who: The course is aimed at graduate students and other researchers. No prior knowledge of RNA-seq analysis tools presented at this workshop is needed. However, it is heavily encouraged to have a level of familiarity with R and UNIX.
Where: Heritage Hall Room 104 (1401 University Blvd, Birmingham, AL 35233)
When: July 09-10, 2024
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. Please see the installation instructions to ensure all required tools and packages are setup prior to the workshop.
If you have any questions or errors while installing any of the software or packages or during any of the setup, please attend one of the below sessions for troubleshooting. The dates and times for these more focused are listed below, and the Zoom link is available here.
July 2nd: 2pm - 2:30pm
July 8th: 11:30am - 12pm
Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email kdaughtry@uabmc.edu for more information
Roles: The roles for this workshop (who will be doing what) will be the same as the roles present in a Software Carpentries workshop. To learn more about the roles, refer the the Software Carpentries Workshop FAQ
We will use this Etherpad document for chatting, taking notes, and sharing URLs and bits of code
| Day 1 | Day 2 | ||
|---|---|---|---|
| 08:00 | Sign-in & Setup | 08:30 | Sign-in |
| 08:50 | Introduction & Welcome Session | 09:00 | Data Assumptions, DEG Analysis, and Annotation |
| 09:00 | Introduction to RNA-Seq Analysis | 10:30 | Morning Break |
| 09:30 | Introduction to nf-core rnaseq | 10:45 | Data Exploration and DEG Visualization |
| 10:30 | Morning Break | 12:15 | Lunch |
| 10:45 | Executing nf-core rnaseq | 13:00 | DEG Visualization (continued) |
| 12:00 | Lunch | 13:30 | Enrichment Analysis & Visualization |
| 12:45 | Reviewing RNASeq Results | 15:00 | Break |
| 14:00 | Break | 15:15 | GSEA Analysis & Visualization |
| 14:15 | Intro to DESeq2 and QC | 16:45 | Wrap-Up & Additional Resources |
| 17:00 | END | 17:00 | END |
Please ensure you follow all instructions on this page.