RNA-Seq Data Analysis  
March 1, 8, 20 2017

Due to inclement weather the third session originally scheduled for March 15 is rescheduled for Monday March 20th 3:30-5:00pm 655 Rhodes Hall.

This 3-session workshop will cover the basic RNA-seq data analysis methods, including read alignment, transcript quantification, differentially expressed gene identification, and downstream clustering and function/pathway analysis. Each session will include one hour lecture, followed by 30-minutue hands-on time.  Workshop attendees will need to bring your own laptop computers to the workshop. (You do not need to have a powerful laptop computer for this workshop, as the laptops would serve as terminals and the real computation will be done on the Bioinformatics Facility's servers.) There will be step-by-step instructions for each exercise, which can be done either at home or at post-lecture hands-on time. The registration fee is $100.

Bioinformatics Facility is organizing 6 workshops in the Spring 2017 - if you'd like to register for all of them at a reduced rate please go to this page.

The workshop will include practical exercises, that can be conducted on your own machine, or on BioHPC Lab workstations especially reserved for the workshop. Our workstations run Linux operating system, so if you are going to use our machines and are new to Linux computing environment you may want to attend our free  workshops "Introduction to BioHPC Lab" and "Linux for Biologists". You can also use both workshop materials posted online to refresh your Linux skills:

Linux for Biologists Part 1   Linux for Biologists Part 2  Linux for Biologists Part 3

Access to BioHPC Lab workstations requires a Lab account. If you do not yet have an account on BioHPC Lab system, we will create one for you. Also, we will assign a machine for you to work on during  the workshop (during and after the sessions). Machine reservations will be active from March 1st until end of the day March 21st.

Machine allocations are posted here.

Workshop Outline
Session 1 3/1/2017 3:30:00 PM 655 Rhodes
Alignment of Illumina RNA-seq reads, visualization and manipulation of the alignment files. Exercise 1: Read mapping with STAR and TOPHAT
Session 2 3/8/2017 3:30:00 PM 655 Rhodes
Quantification and normalization of RNA-seq data; identification of differentially expressed genes. Exercise instructions.
Session 3 3/20/2017 3:30:00 PM 655 Rhodes
Clustering analysis of transcription profiles, and function/pathway enrichment analysis. Exercise instructions.
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