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Genboree Microbiome Workbench 16S Workshop Part I - March 11, 2014

Join us for the Genboree Microbiome Workbench 16S Workshop, held on March 11, 2014. This workshop introduces key workflows for managing microbiome data including how to create groups, databases, and projects. Learn to upload files, create samples using metadata, link samples to sequence files, and perform quality checks with QIIME and RDP. Gain insights into efficient data management practices and the importance of tracking information across multiple users. Visit the Genboree platform for resources and guidelines.

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Genboree Microbiome Workbench 16S Workshop Part I - March 11, 2014

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  1. Genboree Microbiome Workbench 16S Workshop Part I March 11th, 2014 Julia Cope Emily Hollister Kevin Riehle

  2. Genboree Workflow • Create Group • Create Database • Create Project • Upload Files  • Create Samples (Sample Import using metadata file)  • Link Samples to Sequence Files (Sample File Linker)  • QC and Attach Sequences (Sequence Import)  • QIIME    • RDP 

  3. Genboree • URL: http://www.genboree.org • Workbench and Commons Differences • Account • How to create your account? • http://genboree.org/theCommons/ezfaq/show/public-commons?faq_id=493 • Workshop Home • http://genboree.org/theCommons/projects/mw-march-2014

  4. Workbench • Where is it? http://genboree.org/java-bin/workbench.jsp • Create a Group - Demo • Why? To serve as a project base • How to share it with others? • http://genboree.org/theCommons/ezfaq/show/public-commons?faq_id=494 • Create a Database - Demo • Why? To hold processed and pre-processed files • Using folders to organize the space • http://genboree.org/theCommons/ezfaq/show/public-commons?faq_id=491 • Create a Project - Demo • Why? To have a record of the major level processes that you have used on your data • Importance of tracking information for multiple users in a group • http://genboree.org/theCommons/ezfaq/show/public-commons?faq_id=492

  5. Genboree Workflow • Create Group • Create Database • Create Project • Upload Files  • Create Samples (Sample Import using metadata file)  • Link Samples to Sequence Files (Sample File Linker)  • QC and Attach Sequences (Sequence Import)  • QIIME    • RDP 

  6. Upload Files • What to import (upload) • Meta data • .sff (s) • Can both meta data and sffs be in one file? No - upload them separately. .sffs will need unpacking while meta data files will need converting. Shortcutting this step can cause odd problems down the line. • Importing files and choosing to extract will cause the system to queue the process. The process may take a few moments. • Now that I have it uploaded…How to edit and remove files? - Demo

  7. Genboree Workflow • Create Group • Create Database • Create Project • Upload Files  • Create Samples (Sample Import using metadata file)  • Link Samples to Sequence Files (Sample File Linker)  • QC and Attach Sequences (Sequence Import)  • QIIME    • RDP 

  8. Create Samples (Import) • Import samples singly or in multiples • Creating and adding samples to a set • Import Behavior • Assign samples to a set • What is a sample set? • Why use them? • Grouping for downstream analysis • Makes Genboree use faster on user (don’t have to move each file around) • Editing sample information

  9. Create Samples (Import) • Import samples singly or in multiples: Demo • Creating and adding samples to a set • Input Window: Metadata file • Output Window: Target Database • Data> Samples & Sample Sets> Samples> Import Samples • Double check your Input, Target, and Settings • Import Behavior • Create New Record • Keep Existing • Merge and Update Use this one by default • Replace Existing • Assign Samples to new Sample Set • Name the folder or leave blank to not create a set • Can be added to a set later

  10. Create Samples (Import) • What is a sample set? • Why use them? • Grouping for downstream analysis • Makes Genboree use faster on user (don’t have to move each file around) • Editing sample information • What isn’t possible (right now)? • Editing column titles • Adding single samples de novo

  11. Sample Set Management • Demo. adding samples to a sample set • Input Window: Sample to be added • Output Window: Target Sample Set • Data> Samples & Sample Sets> Sample Sets> Add Sample to Sample Set • Demo. editing Sample (or Sample Set) data • Input Window: Sample to be edited • Output Window: Blank • Data> Samples & Sample Sets> Samples> Edit Samples • This is important for later stages • Makes Sequence Import easier and cleaner

  12. Sample Set Management • Editing Sample (or Sample Set) data • Move boxes before saving or you will lose your edit.

  13. Genboree Workflow • Create Group • Create Database • Create Project • Upload Files  • Create Samples (Sample Import using metadata file)  • Link Samples to Sequence Files (Sample File Linker)  • QC and Attach Sequences (Sequence Import)  • QIIME    • RDP 

  14. Link Samples to Sequence Files • Sample file linker tool • The name is opposite the file positions required. • Arrangement in the Input Window: • .sff • Sample Set or • .sff • Sample • .sff • Sample • .sff • Sample • Output Window: Empty • Demo. how to do it and how to check it has been done.

  15. Link Samples to Sequence Files • How to check your linked files? • The prompt screen on linking • The e-mail when complete • The Sample Edit tool – look for fileLocation column. • Demo. looking at linked fileLocation • Input Window: Sample to be edited • Output Window: Blank • Data> Samples & Sample Sets> Samples> Edit Samples

  16. Genboree Workflow • Create Group • Create Database • Create Project • Upload Files  • Create Samples (Sample Import using metadata file)  • Link Samples to Sequence Files (Sample File Linker)  • QC and Attach Sequences (Sequence Import)  • QIIME    • RDP 

  17. Sequence Import • Choose one or more samples to load sequences • Input Window: Sample(s) or Sample Set • Output Window: Target Database • Metagenome> Data Initialization> Import 16S rRNA Sequences • Check quality of import • Fixing the files when something has gone wrong • When it is possible? • When to start over? • Download files from Genboree

  18. Sequence Import • Choose one or more samples to load sequences – Demo. • Input Window: Sample(s) or Sample Set • Output Window: Target Database • Metagenome> Data Initialization> Import 16S rRNA Sequences

  19. Sequence Import • Check quality of import

  20. Sequence Import • Fixing the files when something has gone wrong

  21. Sequence Import • Fixing the files when something has gone wrong • When it is possible? • Bad barcode? • Sample info. wrong? • Primers • Region • Direction • Bad file? • When to start over?

  22. Sequence Import • Download files from Genboree • Click on file • In Details Window, choose Download • Start with • sequences_metrics_ summary.xls • Easy to open • No compression

  23. Sequence Import • When problems arise, check the: • sample.metadata – Does it match what you put in? • fasta.result.tar.gz – Look at the .fasta files • See barcodes • See primers • Notepad for metadata • Bioedit to open fasta • Use WINE on Mac

  24. Genboree Workflow • Create Group • Create Database • Create Project • Upload Files  • Create Samples (Sample Import using metadata file)  • Link Samples to Sequence Files (Sample File Linker)  • QC and Attach Sequences (Sequence Import)  • QIIME    • RDP 

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