Very strange circle from MCScanX

Question

[HZZ0036]

Hi,

I am using MCScanX to compare maize genome and my draft plant genome, which only have scaffolds. I used circle_plotter.java got a very strange circle since I put all of the my scaffolds number in the control_file. How to deal with this like one species have no chromosomes, only have scaff number? Please see the strange circle picture. Does anyone know how to deal with this? Thanks.

Zhang

Answer 1

[Philipp Bayer]

You get this strange circle since you have many, many scaffolds, and you get alignments for all of those tiny circles. The black ring is the names of all scaffolds.

You can't really run this kind of approach with scaffolds, it makes much more sense to run it pseudomolecule by pseudomolecule. You can use MCScanX's gene colinearity results but the pictures are of no use with scaffolds.