Wednesday Aug 15
Lecture: CoGe - Eric Lyons (9:00-10:15)
CoGe (pronounced /k?:j?/ ) stands for Comparative Genomics. It is a online system for making the retrieval and comparison of genomic information and sequence data quick and easy. You can learn more about it at its web site.
Webex Link
- Go to https://iplant.webex.com/iplant/j.php?ED=208539422&UID=1382145847&PW=NZDlkMDI1MGEy&RT=MiM1
- If requested, enter your name and email address.
- If a password is required, enter the meeting password: iPC123
- Click "Join".
Coffee Break (10:15-10:30)
Hands-on with CoGe (10:30-12:00)
Follow one of the two tutorials with different organism focus - if you are familiar with backgrounds, skip introduction and go directly to the step-by-step Methods.
- Brassica (comparison to A. thaliana from Haibao Tang and Eric Lyons)
- Maize (comparison to other grasses, from James Schnable and Eric Lyons)
Lunch (12:00-1:00)
- Take a few minutes to review the following before this afternoon's exercises
- Introductions to metagenomics
- Presentation 1 (Google Doc)
- Metagenomics Intro (PDF 8 MB)
Using the iPlant REST API for powerful bioinformatics (1:00-4:00)
JOIN ME: https://join.me/162-110-033
- Introductory lecture - Dan Stanzione (1:00-1:20)
- Instructor-led tutorial exercise - Using BLASTX against NCBI nr to annotate a metagenomic data set (1:20-2:30)
- Context: We have a set of metagenomic reads from the phyllosphere of soybean, and we want to BLASTX them against NCBI nr.
- Tutorial Material
- Self-guided exercises using the iPlant REST API (2:30-4:00)
- Predicting ORFs from metagenomic assembly
- Taxonomic analysis with MetaPhlan
Catch-up time: SNP annotation, Comparative Genomics, REST metagenomics (4:00-5:00)
- Feel free to take this last hour and catch up on any work you may need to revisit
- Prepare for your group's presentation tomorrow on Genome Assembly and SNP annotation
Conclusion (5:00-)
, multiple selections available,