Frequently Asked Questions
Transfer of data from Strand NGS 2.1 to GeneSpring 13.0 involves exporting the desired experiment from Strand NGS and importing it into GeneSpring:
To export data from Strand NGS 2.1, follow these steps:
● Right-click on the experiment of interest in the Project Navigator
● Select “Export experiment for GeneSpring”
● Select the objects to be exported
● Specify a location to save the .expt file
To import the Strand NGS experiment in GeneSpring 13.0:
● Open the project of interest
● Go to “Project -> Import Strand NGS Experiment”
● Browse for the .expt file
The following types of objects can be exported from Strand NGS 2.1:
● Your selection of read lists, region lists, and data sets,
● By default all sample names, experiment grouping and interpretation information,
● By default all the entity lists and their associated data from analyses like SNP Effect Analysis, for example.
No, experiments cannot be transferred from GeneSpring to Strand NGS.
Samples are imported for the purpose of grouping and interpretation creation in GeneSpring. Using the exported sample information you will be able to create new interpretations in GeneSpring for performing Multi-Omic Analysis .
All aligned reads read list is the master list that contains information on reads available in all the samples. The resulting read lists from any operations are added as child lists to all aligned reads read list. Hence, even if it was unselected during export, the tool creates a new “All aligned reads” read list to which any other child list (user selected list for export) is attached.
However, the number of reads in this new all aligned reads read list would differ. It only includes
read information from the read lists that were selected for export.
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.
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.
The only supported workflow options for imported Strand NGS experiments are Experiment Grouping and Create Interpretation.
No, the two instances of the experiment are stored separately.
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.
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.
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.
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.
Please surrender your NGS license from GeneSpring Help -> License Manager -> Surrender ->Select “GeneSpring NGS” -> ok -> Relaunch the tool and proceed with the Product Update.
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