Q22. I have a file with annotation information for my genes of interest. Can I import them in Genome Browser?

Yes, annotation information present in a file can be imported in GeneSpring. You may use any of the following methods:

Q21. How can I see data distribution over all the chromosomes together?

Data distribution over all chromosomes can be obtained by editing track properties from Right-click operations. Go to Edit track properties -> Chromosome View -> Select feature of interest.
This will show the data for the selected chromosome in Genome browser area. To view all the chromosomes together, go to “Chromosome tab” on the left of Genome Browser.

Q20. Why is the Merge icon grayed out in Genome Browser?

Merge icon is used to bring different tracks together. This option is highlighted when two data tracks are selected and both tracks have only one feature enabled.

Q19. How can I change the sequence of tracks in Genome Browser?

To change the sequence of tracks go to the “Reorder” icon in the icon bar. Following this, select the track of interest and arrange it in the order of preference using up or down arrow.

Q18. Is it possible to export images from Genome Browser?

Yes, you may export images in the following two ways:

  1. Right-click on the track of interest -> Export as -> Image. This will export individual track.
  2. Go to the Tool bar in Genome Browser -> Select “Export selected track as image” -> Select the tracks of interest -> Specific a folder to save images. This feature enables you to export one or more than one track together.

Q17. What happens if I upgrade GeneSpring from GS 11.5.1 to GeneSpring 12. Will the builds created in GeneSpring 11.5 still work?

Yes, the builds will continue to work. The builds from previous version will be called as “Segments”.

Q16. I have downloaded the build of my interest in GeneSpring 12. However, while trying to use Genome Browser in my experiment, it says build does not exist?

The Genome Browser is launched on the organism of your experiment. Check the organism of your experiment to ensure that it is the same as the organism of the build.
To check the organism of an experiment, right-click on the experiment name and select “Inspect Technology”. You have the option to change the organism in the Technology Inspector window.

Q15. I have chromosomal coordinates in the build I created and in my experiment. However, I get a message that my entities of interest do not belong at any chromosome. How is it possible?

The mapping of probes in Genome Browser is done using chromosome number and location. The chromosome number is expected to be in alphanumeric (chr1) or only numeric characters. If the format is alphanumeric then all the alphabets should be lowercase. The error could occur if the chromosome number has uppercase in them.

Q14. Is it possible to view raw data on Genome Browser?

Yes, it is possible to view raw data on Genome Browser using the steps below:

  • Launch Genome Browser
  • Drag and Drop the experiment
  • Select the interpretation and samples or conditions
  • Click ok
  • Right-click on the data track
  • Select “Edit track properties”
  • Select “Raw” in region view
  • Click ok

Q13. I would like to view p-values for my probes in Genome Browser. Is that possible?

Yes, it is possible to view list associated values (p-value, Fold change, etc) on Genome Browser. Please follow the steps below:
• Right-click on the track of interest
• Go to Edit track properties
• The list associated value columns are visible as check boxes in the Edit track properties Dialog. Select the required data and it will be added in the same track as one more feature. Click ok.
List associated values are also shown in the spreadsheet.

Syndicate content