Issues in Microsynteny visualization

[lvyunyunSCI]

Hi guys,

I was using the Microsynteny visualization feature in jcvi (JCVI.graphics.synteny) and found bugs when a fragment of one chromosome in one species connects to more than two chromosomes in another species, Other species do not have multiple chromosomes. Instead, there is still only one chromosome, which gives rise to erroneous interpretations. May I ask how to fix this error?

The examples can be the follows:

#blocks files
"A-1 B-1
A-2 B-2
A-3 B-3
A-4 B-4
"
#bed files;
SPA_Chr1 6 8 A-1
SPA_Chr1 16 18 A-2
SPA_Chr1 26 28 A-3
SPA_Chr1 36 38 A-4
SPB_Chr1 6 8 B-1
SPB_Chr1 16 18 B-2
SPB_Chr2 26 28 B-3
SPB_Chr2 36 38 B-4

[tanghaibao]

@lvyunyunSCI

Perhaps I don't completely understand the issue you have.

The example you give has two chromosomes - SPB_Chr1 and SPB_Chr2.
So there should be a switch between gene B-2 and B-3.
You can fix this manually in the blocks file with place holders

A-1  B-1  .
A-2  B-2  .
A-3  .    B-3
A-4  .    B-4

This way, each column represents a distinct region.