Welcome to the GenomeQuest Documentation Wiki
In the GenomeQuest RNA-Seq workflow, we provide spreadsheets that can be imported in GeneSpring for analysis.
GeneSpring provides statistical tools for fast visualization and analysis of expression data. It's an interactive desktop software for statistical analysis of microarray and RNA-Seq expression data within a biological context.
For more information about GeneSpring, Click here
Example of a GenomeQuest RNA-Seq experiment imported in GeneSpring
Importing a GenomeQuest RNA-Seq spreadsheet into GeneSpring
The first time you import a GenomeQuest RNA-Seq experiment into GeneSpring, you need to create a new GeneSpring "Technology".
It will allow GeneSpring to recognize the layout of the GenomeQuest spreadsheets.
Important: You only need to do that once if you import spreadsheets with the same number of samples, but you'll need to create a new technology if you import spreadsheets with a different number of samples.
In the future, GeneSpring (> GX 10) will automatically recognize the layout without the need of creating a new technology.
Contact us at email@example.com if you are having trouble creating a new technology.
Creating a new Experiment
- The first step is to download the spreadsheet from your GenomeQuest experiment
- You need to create a new Project, or open an existing one in GeneSpring.
- Select Project > New Experiment
- Give a meaningful name to your experiment, and make sure you select Generic Single Color for the Experiment Type, add a description if needed, then click Next
- Select the Technology for GenomeQuest you created (If haven't done that, see below, select your GenomeQuest spreadsheet, called "genespring.txt" (Choose File), then click Next
- Select your Normalization (or none), then click Next
- Select your Baseline option, then click Finish
- You should see your new Experiment in the list
Creating a GQ technology in GeneSpring
The first step in GeneSpring is to define the GQ spreadsheet layout that will be applied to files imported from GQ.
Note that depending on the type of experiment you ran in GenomeQuest, you might need to create several technologies (one per spreadsheet layout, depending on the number of samples). This is necessary because GeneSpring require each technology to be based on a set number of columns.
In the future, GeneSpring (> GX 10) will automatically recognize the layout without the need of creating a new technology. Contact us at firstname.lastname@example.org if you are having trouble creating a new technology.
- Create or Open a project
- In Annotation > Create Technology, select Custom From File, and click Next
- in Step 1: Give a meaningful name to the technology, select Single Color, select the spreadsheet you downloaded from GenomeQuest for sample and annotation, and click Next, as shown below
- in Step 2: Define the format of the spreadsheet, and click Next, as shown below
- in Step 3: Select Take all rows, and Take the first row in the selection as the column header, and click Next
- in Step 5: Select Gene Name as the identifier, and choose custom for Identify signal. set RPKMA and RPKMB as signal, and click Next
- in Step 9: Select Gene Name as Identifier and click Finish
- Now, GeneSpring should show you a "Technology uploaded succesfully" message