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      mRNA-Seq Workshop

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
RNA Sequencing Technologies - Dr. Lutz Froenicke
Support
Using Zoom
Using Slack
Cheat Sheets
Software and Links
Scripts
Prerequisites
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
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

Closing Thoughts

The forest through the trees.

flowchart_mrna.png

Be Consistent

Prerequisites for bioinformatics

The bottom line

Next Steps

My recommendation is to follow all of the instructions again, from the beginning on your own and send emails to training.bioinformatics@ucdavis.edu And we will be responsive to answering questions

Upcoming Workshops

Now in our 13th year of training researchers, the UC Davis Bioinformatics Core invites you to attend one or more of our 2020 workshops. The following workshops are suitable for beginners to advanced researchers, and are also of interest to those with some data analysis experience.

Aug 12 - Aug 14, 2020 Introduction to Single Cell RNA-Seq @ UC Davis
Aug 17 - Aug 19, 2020 Advanced Single Cell RNA-Seq @ UC Davis
Oct 5 - Oct 9, 2020 Bioinformatics: Command Line/R Prerequisites
Nov 30 - Dec 4, 2020 Introduction to Analysis of Epigenetic Data

For more information on these and other events, and to register, go to https://registration.genomecenter.ucdavis.edu/

Previous Workshops available online

If you would like to take a look at the documentation from previous workshops.

Questions?

Contact us at training.bioinformatics@ucdavis.edu

If you receive email directly from training.bioinformatics@ucdavis.edu, you are currently subscribed to one of our announcements lists. To subscribe / unsubscribe from the Bioinformatics Core email lists, please follow the instructions at the bottom of http://bioinformatics.ucdavis.edu/contact-us/.