Genboree Microbiome Workbench
16S Workshop Part I
March 11th, 2014
Julia Cope
Emily Hollister
Kevin Riehle
•
•
•
•
•
•
•
•
•
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 
Genboree
• URL: http://www.genboree.org
• Workbench and Commons Differences
• Account
– How to create your account?
– http://genboree.org/theCommons/ezfaq/show/p
ublic-commons?faq_id=493
• Workshop Home
– http://genboree.org/theCommons/projects/mwmarch-2014
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/publiccommons?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/publiccommons?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/publiccommons?faq_id=492
•
•
•
•
•
•
•
•
•
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 
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
•
•
•
•
•
•
•
•
•
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 
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
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
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
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
Sample Set Management
• Editing Sample (or Sample Set) data
– Move boxes before saving or you will lose your
edit.
•
•
•
•
•
•
•
•
•
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 
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.
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
•
•
•
•
•
•
•
•
•
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 
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
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
Sequence Import
• Check quality of import
Sequence Import
• Fixing the files when something has gone wrong
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?
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
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
•
•
•
•
•
•
•
•
•
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 