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DyogenIBENS / Agora

Algorithm For Gene Order Reconstruction in Ancestors
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How to visualize Agora's results #5

Closed ChenXi1201 closed 2 years ago

ChenXi1201 commented 2 years ago

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 image

DyogenIBENS commented 2 years ago

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 commented 2 years ago

您的来信已收到，我会尽快查看，谢谢陈曦