Actions Panel
RNA-Seq Analysis (Spring 2019)
Date and time
Location
Institute for Genomic Biology
1206 West Gregory Drive, Urbana, IL 61801 Room 607 (in the basement) Urbana, IL 61801Refund Policy
Description
Workshop Description
This 8-part workshop will explain and provide hands-on exercises over:
- RNA sequencing technology and experimental design
- Quality control (QC) steps for pre-processing raw sequences
- Aligning reads to a reference and multiple gene counting methods
- QC and normalization of gene counts in R
- Differential gene expression analysis and visualization in R
- Annotation methods in R
This workshop will be held on 8 Friday mornings throughout the Spring semester from 9am - 12:30pm. Please see calendar on the HPCBio workshop page for exact dates. Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it can be done on any species. This 8-part workshop will cover experimental design, evaluation of sequencing quality, genome alignment, gene count extraction, differential gene expression analysis and downstream data mining. It will also include discussions of what to do if your species lacks gene models and/or a genome.
This workshop is appropriate for all graduate students, post-docs, and researchers. Knowledge of R programming, Linux CLI, and high performance computing on Biocluster is required! We will utilize all three of these skills in this workshop. Please do not show up without these skills or you will slow the workshop down, which is unfair to the other attendees. See FAQ for ways to satisfy these pre-requisites.
FAQs
What are the pre-requisites for the RNA-Seq workshop?
You will need to have a basic understanding and skill in R programming, Linux CLI, and high performance computing on Biocluster2. To fulfill these pre-requisites you can take the following workshops:
Option A (integrated around RNA-Seq workshop):
- Introduction to Linux & Biocluster (February 13th & 15th)
- Introduction to R & Bioconductor (March 27th & 29th)
Option B (starts in January):
- Data Carpentry for Genomics (January 31st and February 1st)
- Introduction to Biocluster (February 15th)
Option C:
- To learn these skills independently, email us for our self-guided learning materials.
- Please plan accordingly and allow at least 9-12 hours to study all the pre-requisites ahead of time, and assume this will need to be spread out over 2+ days depending on how free your schedule is.
What are the dates and times of this workshop?
The workshop consists of 8 Friday mornings (9am - 12:30pm) during Spring semester. Please see calendar on the HPCBio workshop page for exact dates.
How do I pay using a C-FOPAL account number?
Please register as a "Participant (Pay $90 via UIUC account)". During checkout, please provide us with the account number you wish to use for payment. Please note that we are not able to accept grant accounts (those starting with 1-4 and 1-5). If you want to use a grant account, we suggest paying by card and then providing the receipt to your department's business office for reimbursement.
Do I need to bring my own computer?
Windows desktops will be available for every attendee. You may bring your own laptop, but make sure to have the necessary software installed ahead of time. You will be emailed these details before the workshop starts.
What if I need to miss a day of the workshop?
All of the sessions will be recorded (assuming no technical difficulties arise), and necessary materials and slides will be posted on a workshop webpage. However, keep in mind that if you need to miss one of the sessions, you will only have a day to catch up.
When do ticket sales end?
We will stop selling tickets on February 22nd at 9am.
Why have the workshop fees changed?
Thanks to the generosity of the OVCR (Office of the Vice Chancellor for Research) we are able to offer our workshops for a nominal fee. Without this support, the true cost to run such workshops could be hundreds to over a thousand dollars per attendee.
How can I contact the organizer with any questions?
You may email us at hpcbiotraining@igb.illinois.edu for any questions pertaining to training.