How to run microsynteny plotter from McScan?
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6.0 years ago
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I was trying to run microsynteny of Madbox gene family using the McScan tool's family_circle_plotter.java available here (https://github.com/wyp1125/MCScanX/blob/master/downstream_analyses/family_circle_plotter.java ). I followed the manual (http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf ) to run this tool as mentioned using the command

javac family_circle_plotter.java
java  family_circle_plotter -g xyz.gff -s xyz.collinearity -c at_vv_dual_circle.ctl -f madbox_test.txt -o family_plot_output_png.png

using the data available here: https://www.dropbox.com/sh/prsy6d9d8udjer3/AAASODzVUZL7S0WbIMB4nVvwa?dl=0

I was able to plot this https://www.dropbox.com/s/cwzju93rizw47g0/family_plot_output_png.png?dl=0 , it does not highlights the Madbox genes. Could someone please help me why it is not highligting the microsynteny for this gene family? Thank you for your help in advance.

Mcscan microsynteny • 2.4k views
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5.8 years ago

It could be because of the wrong format of the Madbox_genes file. A madbox_gene family file should be in tab-delimited format with gene family name in the first column. Refer to this link https://github.com/wyp1125/MCScanX for the format which is mentioned under the subheading 9)detect_collinearity_within_gene_families.pl.

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Hey

I followed and used the example data of Arabidopsis but still not able to make the genes name visible on circle. What could be the reason ?

Script used :

java family_circle_plotter -g at.gff -s at.collinearity -c family.ctl -f at_MCL_families.txt -o at_circle_jpeg_file

Any clues or point will be helpful. Tnks

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