Classes
- The Basic Bioinformatics Tools Workshop Series offered through Bioinformatics@HSL provides seminar and hands-on computer workshops on bioinformatics tools and resources to faculty, staff and students of UNC-Chapel Hill. Below are the list of workshops offered for Fall 2020. Visit Bioinformatics@HSL for details and registration information on the workshops.
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Basic Bioinformatics Tools Workshops – Fall 2020
The Fall 2020 Basic Bioinformatics Tools Workshops will be delivered online via Zoom. Email me if you would like to be added to the list to receive announcements about these workshops.
Registration Now Open for Introduction to the UNIX Shell: A Six Workshop Sequence:
1. UNIX Shell Basics 1 (Online via Zoom) 9/1/2020, 2:00pm – 3:00pm Details | Register
2. UNIX Shell Basics 2 (Online via Zoom) 9/1/2020, 2:00pm – 3:00pm Details | Register
3. Working with Files (Online via Zoom) 9/1/2020, 2:00pm – 3:00pm Details | Register
4. Useful Tools and Pipes (Online via Zoom) 9/1/2020, 2:00pm – 3:00pm Details | Register
5. Loops and Scripts (Online via Zoom) 9/1/2020, 2:00pm – 3:00pm Details | Register
6. Introduction to Slurm (Online via Zoom) 9/1/2020, 2:00pm – 3:00pm Details | Register
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Introduction to the UNIX Shell: A Six Workshop Sequence
The six, one-hour Introduction to the UNIX Shell workshops immediately below are a chained sequence of workshops to introduce participants to the UNIX command line, basic commands, navigating the file system, setting up bioinformatics projects, and introductory scripting. Each class will build upon the prior class and each part is a prerequisite for the next class in the six-workshop UNIX Shell sequence.
The six workshops in the UNIX block are in turn prerequisites for the five, one-hour Introduction to Bioinformatics Basics workshops which follow in the entire eleven workshop series.
1. UNIX Shell Basics 1 (Online via Zoom) – Completed
Time: Tuesday 9/1/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: You will need an account on the “Longleaf” Linux cluster managed by ITS Research Computing. Follow instructions for requesting a “Longleaf” account on the ITS Research Computing website: https://its.unc.edu/research-computing/request-a-cluster-account/. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.
Prerequisites: No prior knowledge of UNIX is required.
2. UNIX Shell Basics 2 (Online via Zoom) – Completed
Time: Tuesday 9/8/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
UNIX Shell Basics 1
3. Working with Files (Online via Zoom) – Completed
Time: Tuesday 9/15/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
UNIX Shell Basics 1
UNIX Shell Basics 2
4. Useful Tools and Pipes (Online via Zoom) – Completed
Time: Tuesday 9/22/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
UNIX Shell Basics 1
UNIX Shell Basics 2
Working with Files
5. Loops and Scripts (Online via Zoom) – Completed
Time: Tuesday 9/29/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
UNIX Shell Basics 1
UNIX Shell Basics 2
Working with Files
Useful Tools and Pipes
6. Introduction to Slurm (Online via Zoom) – Completed
Time: Tuesday 10/6/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites: UNIX Shell Basics 1
UNIX Shell Basics 2
Working with Files
Useful Tools and Pipes
Loops and Scripts
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Introduction to Bioinformatics Basics: A Five Workshop Sequence
This five-workshop sequence will cover bioinformatics data types, basic quality control of short read data including assessing quality and filtering data, and basic bioinformatics methods including how to align data to a reference genome and call variants. Time permitting, some scripting will be covered as well.
The six workshops in UNIX Shell sequence above are prerequisites for the five-workshop Introduction to Bioinformatics Basics sequence. Additionally, each class in the Introduction to Bioinformatics Basics sequence will build upon the prior class and each session is a prerequisite for the next class in the sequence.
7. Intro to Bioinformatics Basics: Quality Control and Trimming (Online via Zoom) – Completed
Time: Tuesday 10/13/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
The six workshops in UNIX Shell sequence above (UNIX Shell Basics 1, UNIX Shell Basics 2, Working with Files, Useful Tools and Pipes, Loops and Scripts, and Introduction to Slurm)
8. Intro to Bioinformatics Basics: Aligning Reads (Online via Zoom) – Completed
Time: Tuesday 10/20/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
9. Differential Expression Analysis: Intro and Counting (Online via Zoom) Register
Time: Tuesday 10/27/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
Intro to Bioinformatics Basics: Aligning Reads
10. Differential Expression Analysis: DESeq Basics (Online via Zoom) Register
Time: Tuesday 11/3/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
Intro to Bioinformatics Basics: Aligning Reads
Differential Expression Analysis: Intro and Counting
11. Differential Expression Analysis: Intermediate DESeq & RStudio (Online via Zoom) Register
Time: Tuesday 11/10/2020, 2:00pm – 3:00pm
Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via ZoomAccount Requirement: See UNIX Shell Basics 1 Account Requirement above.
Prerequisites:
The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
Intro to Bioinformatics Basics: Aligning Reads
Differential Expression Analysis: Intro and Counting
Differential Expression Analysis: DESeq Basics
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