New to Circos and how to use gbk file as a source

[Alexander Franca Fernandes]

Hi,

I have a gbk file and I would like to generate a Circos map for that.

The file is attached.

Since I'm new to Circos I have no clue about what should I do.

Could someone help me?

[]s
Alex

[Martin Krzywinski]

What do you want to draw? There are many features in the gbk file.

Your karyotype would be something like

chr - myco myco 0 4340116 black

and if you want to draw genes using highlights, you'd have something like

myco 5123 7262

in the input data file for the highlight and

myco 5123 7267 gyrB tag=BCGM_0005

in the input file for the text track that provides the labels for the genes.

Either way, you'll need to parse the gbk file and extract the coordinate positions into the simple

chr start end [value]

format that Circos uses.

You should probably read through the quick start tutorial

http://www.circos.ca/documentation/tutorials/quick_start/

to get a sense of how Circos works. This will go a long way to helping you answer the question.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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