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Creating A Virtual Reads Database
Here we describe how to create a virtual database made of multiple NGS reads databases. Creating virtual databases for filtered reference databases is much simpler and covered here.
One example where you might need to do this is: You have uploaded and processed different NGS sequence files. Now you would like to combine them into a single virtual database so as to use as input in GenomeQuest's RNA-Seq workflow.
The trickiest part in the whole process is getting the needed sequence databases in one place so as to browse them together.
Step 1: Get the Reads Databases Together
Reads databases are generated by the Reads Processing workflow. You process a raw file of NGS reads to create a sequence database of reads. There are then three entities in this whole chain of events:
- Raw Reads File: This is the file that you obtained from your sequencer and uploaded to GenomeQuest. The name of the file is whatever you supplied when you uploaded it. The file is listed in the "My uploads" area of the My GenomeQuest page.
- Reads Processing Workflow: In order to prepare the reads in your file for further analysis, you run the Reads Processing workflow. Since the NGS reads can be in multiple formats coming from different sequencing platforms, this intermediate step is essential to get the reads into a format that GenomeQuest can analyze. The name of the workflow is what you specified on the launch page when you ran the workflow. The workflows are listed in the "My Data" section of the My GenomeQuest page and are marked off with a cogwheel icon.
- Sequence Database: this is created by the reads processing workflow and is also available in the "My data" section of the My GenomeQuest page.