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      Introduction to the Command Line for Bioinformatics

Introduction to the Workshop and the Core
Cheat Sheets
Windows 10 and Mac installation
Introduction to the Command Line 1
Introduction to the Command Line 2
Introduction to the Command Line 3
Day 3 Homework Solution
Closing thoughts
Github page
Biocore website

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


Introduction to the Command Line for Bioinformatics
June 1st, 2nd, and 4th, 2021 2 p.m. - 5:00 p.m.
Organizer - Bioinformatics Core
Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

Get off to a good start in bioinformatics with this three-part online workshop in the use of the command line interface. This workshop lays the foundation for successful bioinformatics experiments, including RNA-Seq, single cell RNA-Seq, genome assembly, GWAS, variant analysis, epigenetics and more.

This workshop consists of three half-day sessions, combining lecture and exercises in a survey of the basics of the command line for bioinformatics. Completion of this material will allow participants to get the most out of our other experiment-centric workshops. We recommend this course for all beginners.

Introduction to the Command Line for Bioinformatics is scheduled from 2:00 pm to 5:00 pm on Monday, June 1st, Tuesday, June 2nd, and Friday, June 4th.

Participants must have a Mac, a Linux machine, or Windows 10.

The registration fee is $300 for UC students, postdocs, staff and faculty, $450 for Non-UC academic or non-profit participants and $600 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment. We are pleased to be able to offer three group pricing bundle options for labs with multiple registrants: 15% off registration for groups of 3-5, 25% off registration for groups of 6-10, and custom instructional packages for groups larger than 10. If you are interested in one of these pricing options, please contact us at training.bioinformatics@ucdavis.edu for a custom coupon code.

Registration closes on May 31st, 2021.


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 an enthusiasm for learning bioinformatics data analysis.

What do I need? … You will need 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. Windows PowerShell, Terminal or iTerm2 on a Mac, or Bash for Linux), as well as a reliable internet connection. If your department does not allow you to install software on your computer, please contact us ahead of time.

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

How do I apply? … All registration is “first-come, first-served”. There is no application process. 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


Register for Introduction to the Command Line for Bioinformatics at the Genome Center Event Registration site.