Question: Very strange circle from MCScanX
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gravatar for HZZ0036
2.7 years ago by
HZZ003610
HZZ003610 wrote:

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 enter image description here

sequence genome • 1.2k views
ADD COMMENTlink modified 2.7 years ago by Philipp Bayer6.6k • written 2.7 years ago by HZZ003610
0
gravatar for Philipp Bayer
2.7 years ago by
Philipp Bayer6.6k
Australia/Perth/UWA
Philipp Bayer6.6k wrote:

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.

ADD COMMENTlink written 2.7 years ago by Philipp Bayer6.6k
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