Circos Plot for synteny file

Question

[tothepoint]

Dear Friends, I am having trouble with synteny plot. Please share your experience in how you make the coordinate file for your synteny plot. I am trying to make coordinate file look like:

>1

first.chr1:1111111-4444444

second.chr4:33333333-7777777

>2

first.chr1:2222222-9999999

second.chr9:4343545-6548589

I have genome assembly file for the same and want to create the circos map.

Answer 1

[Vitis]

On way to do this is to lay out the chromosomes from two genomes into left and right panels, then draw connections/links based on synteny relationships between chromosomes across genomes. See Fig. 2 from the Canola genome paper published in 2014.

https://science.sciencemag.org/content/345/6199/950