The 2013 RNA-Seq Workshop: From Pipette to P-value!

UC Davis Bioinformatics Training Program

Bioinformatics courses, boot camps and workshops presented by the University of California, Davis Bioinformatics Core

The 2013 RNA-Seq Workshop: From Pipette to P-value!

This exciting RNA-Seq Workshop will include both lab bench and bioinformatics instruction in parallel tracks, both aimed at those seeking more experience with RNA-Seq experiments. Workshop attendees may register for either the “Bench” or “Computer” focused track, but both tracks will involve analysis of RNA-Seq data.

Bench track attendees will spend two half-days working at the lab bench, preparing Illumina libraries from mRNA samples, in preparation for sequencing on an Illumina MiSeq. They will also join the rest of the class for lectures on Illumina Sequencing Technology and the RNA-Seq experimental workflow, and will have the opportunity to analyze RNA-Seq data using Galaxy ( The Bench track will be limited to 16 attendees, due to lab space and material limitations.

Computer track attendees will get a bootcamp-style introduction to bioinformatics analysis on the unix/linux command line, in addition to analysis using Galaxy. Computer track attendees will receive the same fundamentals and workflow lectures as Bench track attendees, but will not be able to participate in lab activities. The Computer track will be limited to 45 attendees.

Note: The Bench track will not involve any command-line instruction. The Computer track will not involve any “lab bench” instruction. Both tracks will include RNA-Seq data analysis using the Galaxy platform.

Prerequisites: Bench track attendees should have basic familiarity with lab safety principles and activities, such as pipetting, measuring, etc. Computer track attendees should have an interest in learning some basic proficiency using the Unix/linux command line for data analysis.

Schedule (9am – 5pm; may run late for Bench track):

Monday, Sept. 9:

  • Morning:  Introductory lectures on Illumina Sequencing, RNA-Seq Experimental Design and overall workflows for both the Bench and Computer tracks.
  • Afternoon:
    • Bench track: Sample QC & polyA Isolation
    • Computer track: Unix Command Line Mini-Bootcamp

Tuesday,  Sept. 10:

  • Morning:
    • Bench track: Remaining Library Prep (end repair, ligation, library QC)
    • Computer track: Command-line RNA-Seq  (read QC, alignment, counting, differential expression testing)
  • Afternoon:
    • Both tracks:
      • Galaxy Introduction
      • RNA-Seq Workflow & Analysis in Galaxy
    • Bench track: Load MiSeq, Start Sequencing!

Wednesday, Sept. 11:

  • All day, both tracks: Galaxy or command-line RNA-Seq Analysis using hot-off-the-sequencer reads!


All bench track and computer track activities will be located at the UC Davis Genome Center, located on the main UCD campus.  For those attending the ICG Americas conference the following days, please be sure to plan ahead for transportation to the workshop.


All participants will need to bring a laptop for use in the bioinformatics portions of the course.  Having linux or mac os installed is suggested, but not required.


For questions on the bench track, contact Ryan Kim of the DNA Technologies Core.

For questions on the computer track, contact the Bioinformatics Core.

Register for the Computer track.

Register for the Bench track.

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