How to run microsynteny plotter from McScan?

Question

[MAPK]

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.

Answer 1

[annapragada.harika]

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.

[Nelo]

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