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      mRNA-Seq Workshop

Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
RNA Sequencing Technologies - Dr. Lutz Froenicke
Using Zoom
Using Slack
Cheat Sheets
Software and Links
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Data Reduction
Files and Filetypes
Prepare dataset
Preprocessing raw data
Indexing a Genome
Alignment with Star
Generating counts tables
Alignment/Counts with Salmon (Extra)
Data analysis
Prepare R for data analysis
Annotation from BioMart
Differential Expression Analysis
Pathway Analysis
Comparison between STAR and Salmon
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

All documentation for the workshop is best viewed from the github.io pages


June 1, 2020 - June 4, 2020, 9 a.m. - 5:00 p.m daily. online learning

July 27, 2020 - July 31, 2020, 9 a.m. - 5:00 p.m daily. online learning

Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

This workshop will include a rich collection of lectures and hands-on sessions with individualized instructor support, covering both theory and tools associated with RNA-seq data analysis. Participants will explore experimental design, technology usage, cost estimation, data generation, and analysis (command-line and R) of RNA-Seq data, generated from the Illumina sequencing platform. Participants will use software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed with provided datasets.

Participants must have access to a computer with a recent version of R, Rstudio, and Java installed, and an application that allows them to ssh into a server (e.g. Bash for Windows, or Terminal for Apple), as well as the ability to connect to the internet.

There are no additional prerequisites other than basic familiarity with genomic concepts and RNA sequencing and analysis. This workshop will be held twice in 2020 online via Zoom (June workshop) and will run from 9:00am to 5:00pm each day with an hour break for lunch.

Participants must supply their own laptop/desktop with a reliable connection to the internet. The labtop/desktop should have a current versions of R version 4.0, Rstudio, and an application that allows them to ssh into a server (see this page)


Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … There are no prerequisites other than familiarity with general biological concepts and an enthusiasm for learning bioinformatics data analysis. Some familiarity with the command-line and R is desirable. However, we will dedicate time to bringing everyone up-to-speed to be able to run the commands needed during this workshop.

What do I need to bring? … You will need to bring your own laptop to use, and an application that will allow you to ssh into a server (e.g. Bash for windows, or terminal for Apple OSX). Computational exercises will be performed on a remote server. We can help with setup early on in the workshop. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.

Can I bring my own data? … We will provide datasets for use during the workshop, as this helps to keep the workshop moving. There may be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How much does it cost? … The registration fee is $1,500 for current students, postdocs, staff and faculty at Univeristy of California campus’ or UC National Labs (LBNL, LANL, LLNL), $1,750 for other academic or non-profit participants and $2,500 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.

How do I apply? … All registration is “first-come, first-served”. There is no application process. So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies? … Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.


If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu


For the remote/virtual course in June.

For the remote/virtual course in July.