circos plot

[#1]

Does anyone know how to make a circos plot for synteny analysis using JMP Genomics?

[#2 · Accepted solution]

Hello,

It is possible. To make one, use the Genome Browswer under Genome Views.  Here is a link to the documentation:

https://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=ST...

The key will be to use the Link Tab in the dialog for this process. Here is a link with a couple more details:

http://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=PA_...

A good example of what you will need is shown by clicking on the "Load" button at the bottom of the dialog and chosing the AffyHuEx1Circular example settings.  This will show some example settings and an example Links SAS Input Data Set that you can open to see what you will need to make the links between the chromosomes.

If you need more, you might want to contact support@jmp.com.

Thanks,

Chris Kirchberg