Contents 1 Merging Your databases into a Virtual Database (VDB): 2 Use Cases: 3 Understanding Virtual Databases in GenomeQuest: 4 How do I distinguish a physical sequence database from other databases in GenomeQuest? 5 Merging Physical Sequence Databases into Virtual Databases (VDBs):

Merging Your databases into a Virtual Database (VDB):

• GenomeQuest provides the ability to merge your physical sequence databases into a conglomerate Virtual Database (VDB), which allows one to utilize a number of GenomeQuest workflows to analyze your merged databases together as opposed to individually.

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Use Cases:

• I have multiple samples from multiple biological replicates that I want to analyze using the RNA-Seq workflow, and so I must merge them into a single database.
• I have a large number of sequences from multiple whole-genome resequencing applications, and would like to map them and call variants with higher coverage, which will give me greater accuracy in SNP and Indel detection when using the Whole Genome Variant Calling Workflow.
• I have ChIP-Seq experiments, and would like to merge my samples from two different ChIP-Seq applications to better detect my protein's binding sites.

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Understanding Virtual Databases in GenomeQuest:

• GenomeQuest has three types of databases:
  • Sequence databases - These consist of unmapped sequences. These are interacted with through what GenomeQuest calls our Sequence Database Browser. This is a type of physical sequence database.
  • Results databases - These consist of mapped sequences. These are interacted with through what GenomeQuest calls our Results Database Browser. This is a type of physical sequence database.
  • Virtual Databases - These are created by merging multiple Physical Sequence Databases into one larger, conglomerate database; a Virtual Database (VDB).

• IMPORTANT NOTE - GenomeQuest allows one to merge only physical sequence databases.

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How do I distinguish a physical sequence database from other databases in GenomeQuest?

• When logging into GenomeQuest, one can view their results by clicking on their "My Data" folder:

• In order to distinguish physical sequence databases from workflow results, GenomeQuest identifies them in the interface via a cog-wheel icon for workflow results, and a disk icon for a physical sequence database:

• What if you want to isolate or filter for all your physical sequence databases? Great question!! Use the Search Tool in the upper-left corner of your GenomeQuest dashboard:

• Once the search button is clicked, it will expand to present you with a set of fields and keywords that are searchable.
• Perform these next steps to get all your physical sequence databases:

1. Uncheck Folder, and keep Seqdb and Workflow checked.
2. Next, ensure "In folder:" is set to Selected (My Data).
3. Finally, choose the fields 'sequence database type', 'equals', and seqdb.
4. Now hit 'Apply'.

• Now you have a list of all of your physical sequence databases:

• Now comes the fun part- Merging some of your physical sequence databases into a larger Virtual Database.

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Merging Physical Sequence Databases into Virtual Databases (VDBs):

• Once you have identified your physical sequence databases, you can now merge them. Let's start to merge them by selecting the check-boxes next to the runs we're interested in:

• Once clicked, you can now select the "Browse Sequence Databases" button above:

• That is it! Next, you will be taken to GenomeQuest's sequence database browser where you can simply click 'Result' > 'Save as Virtual Database':

• Now just give your virtual database a name, and description. You have now created a VDB. Congrats!

• As you can see, it will now show up under your "My Data" folder: