Data Carpentry Genomics at the University of Nebraska at Omaha


Setup Download files required for the lesson
Day 1 00:00 1. Data Tidiness How to collect and structure the data about your sequencing data
00:30 2. Planning for NGS Projects How to plan and organize your data for a genome sequencing project
01:00 3. Examining Data on the NCBI SRA Database How to work with public data in the NCBI SRA
01:30 Finish
Day 2 00:00 4. Introducing the Shell What is a command shell and why would I use one?
How can I move around on my computer?
How can I see what files and directories I have?
How can I specify the location of a file or directory on my computer?
00:30 5. Navigating Files and Directories How can I perform operations on files outside of my working directory?
What are some navigational shortcuts I can use to make my work more efficient?
01:20 6. Working with Files and Directories How can I view and search file contents?
How can I create, copy and delete files and directories?
How can I control who has permission to modify a file?
How can I repeat recently used commands?
02:05 7. Redirection How can I search within files?
How can I combine existing commands to do new things?
02:50 8. Writing Scripts How can we automate a commonly used set of commands?
03:30 9. Project Organization How can I organize my file system for a new bioinformatics project?
How can I document my work?
04:00 Finish
Day 3 00:00 10. Assessing Read Quality How can I describe the quality of my data?
00:50 11. Trimming and Filtering How can I get rid of sequence data that doesn’t meet my quality standards?
01:45 12. Variant Calling Workflow How do I find sequence variants between my samples and a reference genome?
02:45 13. Automating a Variant Calling Workflow How can I make my workflow more efficient and less error-prone?
03:30 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.