USF Genomics

USF Genomics Program Training

The USF Genomics Program offers two types of training workshops, the RNA-seq Illumina Sequencing Laboratory Workshop and the RNA-seq Data Analysis Computational Workshop. Each workshop is offered three times a year. These workshops are open to all in the USF community and required for access to use the USF Genomics shared equipment.

  • RNA-seq Illumina Sequencing Laboratory Workshop


    This 5-day intensive hands-on training to enables participants to confidently prepare high-quality sample libraries for sequencing.


    This training course includes presentations on technology theory and practical experience with entire laboratory sample prep workflow. Experienced trainers will lead you through using TapeStation and Miseq equipment. By the end of this training, you will be able to: complete Illumina library preparation process and  set up a sequencing run using Illumina Miseq Control Software.

    Participant Requirements

    • To maximize effectiveness, this training is limited to 6 participants at a time.  
    • A basic knowledge of biochemistry and molecular biology and familiarity with laboratory equipment usage are pre-requisites.  
    • Participants will need to bring your own micropipettes (10µl, 200µl and 1000µl) 
    • Participants may use this to test their own experimental samples, each      participant can prep two samples.sequence analysis or command line experience are not required. 

    Workshop Structure:

    Day 1 (Friday): Illumina sequencing technology introduction (open to non-registered participants)
    Day 2 (Monday): Illumina sequencing technology overview and RNA sample prep
    Day 3 (Tuesday): Library Prep (1) - mRNA purification, 1st, 2nd strand cDNA synthesis
    Day 4 (Wednesday): Libarary Prep (2) - A-Tailing, ligation, PCR amplification, Beads purification
    Day 5 (Thursday): qPCR quantification, Normalize & pool, Set up Miseq run, Base-Space
  • RNA-seq Data Analysis Computational Workshop


    This 5-day in-depth course will instruct participants on the theoretical and practical concepts related to RNA sequencing analysis, enabling them to perform these analyses independently.


    The first workshop module is an introduction to data analysis using Linux, assuring that all participants are able to follow the practical parts. The second module discusses advantages and disadvantages of current sequencing technologies and their implications on data analysis. The third module introduces preprocessing raw reads, read mapping, visualization of mapped reads and one proceeds with first hands-on analyses (QC, mapping, visualization). The fourth module introduces ‘R’ a programming language to perform statistical computing  and visualization, and ‘Bioconductor’ an R based toolshed for analyzing genomic data. The last module addresses quantification of gene expression and predict differentially expressed genes, followed by a whole day hands-on RNA-Seq analysis pipeline: TUXEDO protocol.

    Participant Requirements

    • Admittance to the course is limited to 10 participants.
    • A basic knowledge of biochemistry and molecular biology, a basic familiarity with computer usage and a need for RNA sequence analysis for current ongoing research are recommended pre-requisites.
    • Participants will be required to complete an online module prior to workshop.
    • Participants will need to have their own laptop to access the USF     research Computing  infrastructure for hands-on sessions.
    • Prior sequence analysis or command line experience are not required. 

    Workshop Structure

    Day 1 (Friday): Illumina Sequencing Introduction & Computer and Software Check (open to non-registered participants)

    Day 2 (Friday): Illumina Sequencing Refresher & Linux for Bioinformatics

    Day 3 (Monday): Introduction to RNA sequencing & RNA-seq Alignment and Visualization

    Day 4 (Tuesday): Introduction to R and Bioconductor & Expression and Differential Expression

    Day 5 (Wednesday): RNA-seq - TUXEDO Pipeline Hands-onWorkshop Structure

  • Registration

    Click here for Online Registration 

    If you have questions regarding the USF Genomics Workshops, email 

    Due to enrollment caps, there is a waitlist for the USF Genomics Workshops. You will be contacted after registering about the next available workshop.