How to visualize Agora's results

[ChenXi1201]

Hello, the species I want to study is not on Genomicus, so I used Agora to analyze, I want to know how to use the results of Agora to draw the picture like 'Karyotype View with ancestors' in Genomicus. Have you developed corresponding R package or tools？Thanks

[DyogenIBENS]

Hello,
thank you for using AGORA and Genomicus.
At the present time, we do not provide tool to generate such global view with command line.
However, you can use src/misc.compareGenomes.py to generate the karyotypes one by one (with the option mode=drawKaryotype).

The first ancestral karyotype (one color per ancestral block) can be generate by comparing the genome to itself, eg:
src/misc.compareGenomes.py ancGenome.A1.list.bz2 ancGenome.A1.list.bz2 ancGenes.A1.list.bz2 -mode=drawKaryotype > A1.ps

The others, by comparing the genome (ancestral or modern) with the first ancestral one:
src/misc.compareGenomes.py genome.M1.list.bz2 ancGenome.A1.list.bz2 ancGenes.A1.list.bz2 -mode=drawKaryotype > M1.ps

etc...
options are available (+sortBySize, -minChrSize etc...)

I hope this allows you to do what you want on your data,
Best wishes,
Alexandra

[ChenXi1201]

您的来信已收到，我会尽快查看，谢谢陈曦