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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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request for your help to understand the syntheny plot #49

Open amit4mchiba opened 2 years ago

amit4mchiba commented 2 years ago

Hi,

I am new to comparative genomics and I am going to ask a very stupid question. I am so sorry for that. I am working on two vertebrates and assembled a genome for two close species. When I performed synteny analysis using MCSCANX and plotted, I could see a inverted synteny block for Gg_chr5 image

Does this means that this is an assembly error as the rest of all chromosomes are linear and nice, or could it mean that this is a biological discovery? If this is an error, how can I find the coordinates at which I could change the orientation for this scaffold?

I am again so sorry for this stupid question and will be grateful if you could advise me.

regards Amit

kuowenhsi commented 2 years ago

The question is not stupid. but based on the information here, I am not able to tell you whether it is an error or a biological discovery. You need HiC or linkage map to help you figure it out. If you then find it is an assemble error, you can source your agp file and split the scaffold to correct it.