Q15. Can I install GeneSpring 13.0 on the same computer as GeneSpring 12.6.1?
Yes, you can install both versions of GeneSpring on the same system. However, you will have to change the ports on which each version will be running. To change the port for GeneSpring 13.0, please follow the steps below:
a. Navigate to the GeneSpring 13.0 installation directory
b. Go to \app\PostgreSQL\data folder
c. Open the postgresql conf file with a text editor program
d. Change the port. For example: port = 5438
Q14. I do not have any NGS experiments in GeneSpring. However, it doesn’t allow me to update the product to GeneSpring 13. How do I proceed?
Please surrender your NGS license from GeneSpring Help -> License Manager -> Surrender ->Select “GeneSpring NGS” -> ok -> Relaunch the tool and proceed with the Product Update.
Q13. I have an unused purchased GeneSpring NGS license and now I would like to create NGS experiments. How should I proceed?
Please analyze your NGS data in Strand NGS. Contact the GeneSpring team with your GeneSpring NGS Order ID to get a corresponding Order ID for Strand NGS 2.1.
Q12. I have created NGS experiments in GeneSpring NGS. Can I access them and use GeneSpring 13.0 features in parallel?
To continue accessing NGS projects in GeneSpring, please follow the steps below:
a. Do not update GeneSpring 12.6.1
b. Send your Order IDs to the GeneSpring team at informatics_support [at] agilent [dot] com. You will be provided with Order IDs for GeneSpring 13.0 and Strand NGS 2.1. The validity of these Order IDs will be the same as your current Order IDs.
c. Install GeneSpring 13.0 and Strand NGS 2.0 and activate both softwares with above provided Order IDs.
Going forward please analyze your NGS data in Strand NGS 2.1.
Q11. How can I add an existing pathway to an imported NGS experiment?
To add a pathway, follow these steps:
● Go to “Search -> Pathways”
● Select the pathway of interest
● Click the “Add selected pathways as pathway list to active experiment” icon.
Q10. Is the hierarchy of read lists maintained when a .expt file is imported into GeneSpring 13.0?
If the parent list for a read list is exported then you will see the same hierarchy in the imported experiment. Any read list that was selected without its parent read list will become a child list of the “All Aligned Reads” read list.
Q9. Is an experiment overwritten if it is imported twice?
No, the two instances of the experiment are stored separately.
Q8. What are the workflow options available for experiments imported from Strand NGS?
The only supported workflow options for imported Strand NGS experiments are Experiment Grouping and Create Interpretation.
Q7. I have imported a Strand NGS experiment. However, I get the error message that the build is not supported. How do I fix this?
This can be fixed by downloading the relevant build in GeneSpring 13.0. To download the build go to “Annotations -> Annotations Manager -> From server -> Select the build of interest and download it”. You may want to download the Gene and Transcript model as well to aid in data visualization.
Q6. What are the pre-requisites for importing a Strand NGS experiment?
You have to have the same organism and build downloaded in GeneSpring 13.0 that was used for experiment creation in Strand NGS 2.1.
