The Bioinformatics Core Research Facility (BCRF) and the Holland Computing Center (HCC) are organizing a joint introductory workshop to HCC resources and 16S Microbial Analysis. These lessons are tailored for beginners and require no previous experience, but some introductionary knowledge in R is preferred. There are many good online tutorials for learning basic R, including the one provided by Software Carpentry.
When: April 14th, 17th and 19th 2023 from noon to 5:00 pm CST.
Where: This workshop will be delivered remotely via Zoom.
Cost: $20 for NU participants / $40 for non NU participants.
For this workshop, attendees will need:
- computer with Internet and SSH connection as this workshop will feature hands-on practice
- free HCC account
Schedule:
Friday, April 14th
noon - 1:00 pm |
Setup and SupportTime available for setting up accounts or troubleshooting issues prior to the day's events. |
1:00 pm - 2:45 pm |
Introduction to HCCGeneral introduction to the services and resources HCC offers. |
2:45 pm - 3:00 pm |
Break |
3:00 pm - 4:45 pm |
Introduction to HCC Open OnDemandLearn about HCC's Open OnDemand instances for browser-based access to Crane and Swan. |
4:45 pm - 5:00 pm |
Open QuestionsTime available for questions about today's events. |
Monday, April 17th
Material links:noon - 1:00 pm |
Setup and SupportTime available for setting up accounts or troubleshooting issues prior to the day's events. |
1:00 pm - 2:45 pm |
Introduction to RLearn about files, dataframes and plotting. |
2:45 pm - 3:00 pm |
Break |
3:00 pm - 4:45 pm |
Introduction to 16S Microbial AnalysisLearn what is a microbiome, what questions can we answer with either amplicon or shotgun sequencing, what are the data structures and tests that we can do or not do. Introduction to dada2 and performing filtering, learning error model and error correction. |
4:45 pm - 5:00 pm |
Open QuestionsTime available for questions about today's events. |
Wednesday, April 19th
Material links:noon - 1:00 pm |
Setup and SupportTime available for setting up accounts or troubleshooting issues prior to the day's events. |
1:00 pm - 2:45 pm |
Introduction to 16S Microbial Analysis - cont.Learn how to make a phyloseq object for further analysis (applying error model, merging sequences, determining ASVs, assigning taxonomy, phylogeny). |
2:45 pm - 3:00 pm |
Break |
3:00 pm - 4:45 pm |
Introduction to 16S Microbial Analysis - cont.Learn to visualize taxonomic abundance, and calculate alpha and beta diversity. |
4:45 pm - 5:00 pm |
Open QuestionsTime available for questions about today's events. |
Please contact us at hcc-support@unl.edu if you have questions or concerns and we will be happy to help!