Plotting two identical karyotypes for comparison

[Allison Galassie]

I am looking to make a plot showing the shared connections between two cell types from the same organism using links. However, when I try to plot even just the ideogram, I get an error that [hs1] is being repeated.

My input for defining the karyotype: karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.human.txt

Error: Chromosome [hs1] defined more than once in karyotype file.

Is there a way to plot two human karyotypes on the same plot without having to make a separate unique karyotype file for each one?

Thanks,

Allison

[Martin Krzywinski]

Yes, you'll have to rename the chromosomes in the second karyotype to something else. Circos requires that each chromosome has a unique name.

If I have two samples with the same genome, I do something like this

# in sample 1

hs1-1

hs2-1

...

# in sample 2

hs1-2

hs2-2

...

Your data files would then look like

# link between hs1 in sample 1 to hs10 in sample 2

hs1-1 50 75 hs10-2 100 150

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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