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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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Circle_plotter prints half circle with higher number of chromosomes #54

Open jgnunes opened 2 years ago

jgnunes commented 2 years ago

Hi,

Fisrt of all, thanks for developing such a nice tool.

I'm having an issue when trying to create circle plots for higher number of chromosomes. For the complete set of chromosomes, I'm having the following "half" printed circle:

mm_lf circle 23

This was generated with the following command: 

java circle_plotter -g mm_lf.gff -s mm_lf.collinearity -c mm_lf.ctl -o mm_lf.circle.png

The CTL file looked like this: 

800     //plot width and height (in pixels)
mm1,mm2,mm3,mm4,mm5,mm6,mm7,mm8,mm9,mm10,mm11,mm13,mm14,mm15,mm16,mm18,lf1,lf2,lf3,lf4,lf5,lf6,lf7,lf8,lf9,lf10,lf12,lf14,lf17  //chromosomes in the circle

Please find attached the COLLINEARITY, GFF and CTL files: mm_lf.gff.gz mm_lf.collinearity.gz mm_lf.ctl.gz

I've noticed that if I decrease the number of chromosomes to 24 or 23 (depending on the chromosomes removed) the circle_plotter script works just fine:

mm_lf reduced circle 05

I was wondering if you have experienced a similar issue and if yes, what could be a possible workaround.

Best wishes,

thesnakeguy commented 1 year ago

How did you even managed to get the .collinearity output from MCScanX. I am using my .blast and .gff (chr gene start stop) as input, but I get 0 matches. Others are reporting the same issue. Your input would help a lot! Cheers