Re: [circos] Circos for gene of bacterial genome

[Martin Krzywinski]

The karyotype file is used to define the genome - number, size and names of chromosomes.

To show gene regions and labels, use highlight and text plots. You can automatically put highlights on the ideograms, like this

http://www.circos.ca/documentation/tutorials/highlights/ideogram_highlights/

This example shows a mock circular genome with different data tracks

http://www.circos.ca/tutorials/lessons/recipes/microbial_genomes/

When you define your karyotype file, make sure that its format is correct. Your version above had an error. The right format is

chr - chr_name chr_label start end color

e.g.

chr - chr1 1 0 1000 black

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Sun, Feb 10, 2013 at 7:08 PM, Mattos <matt...@yahoo.com.br> wrote:

Hy, Please, I would like to use circos for gene label in bacteria, I'am  specifying the position and name, and I would like  to put links between distinct genes. But, in configuration Karyotype, Right at the start, in the configuration of karyotype is giving error. One example:

My archive Karyotype.txt, hypotethical:

chr -  geneX 120000 114400.

Please,  If anyone ever had the same problem and can help me,

I will be grateful for any help you can provide.

Leandro

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[Charitra Mishra]

Dear Dr Martin
I am almost beginner with Circos, but I am able to make circos plot for showing fusions between chr1 and chr2. It was just easy :)
My problem is that It does not show the gene name (I have to manually add the gene names in .png)
My fusion.txt file:
hs2 184472606 184472606 hs1 174973789 174973789

Is there any way that it can show the gene names?
thank you

On Wednesday, February 13, 2013 5:01:11 AM UTC+9, Martin wrote:

The karyotype file is used to define the genome - number, size and names of chromosomes.

To show gene regions and labels, use highlight and text plots. You can automatically put highlights on the ideograms, like this

http://www.circos.ca/documentation/tutorials/highlights/ideogram_highlights/

This example shows a mock circular genome with different data tracks

http://www.circos.ca/tutorials/lessons/recipes/microbial_genomes/

When you define your karyotype file, make sure that its format is correct. Your version above had an error. The right format is

chr - chr_name chr_label start end color

e.g.

chr - chr1 1 0 1000 black

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Sun, Feb 10, 2013 at 7:08 PM, Mattos <matt...@yahoo.com.br> wrote:

Hy, Please, I would like to use circos for gene label in bacteria, I'am  specifying the position and name, and I would like  to put links between distinct genes. But, in configuration Karyotype, Right at the start, in the configuration of karyotype is giving error. One example:

My archive Karyotype.txt, hypotethical:

chr -  geneX 120000 114400.

Please,  If anyone ever had the same problem and can help me,

I will be grateful for any help you can provide.

Leandro

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[Martin Krzywinski]

Answered in this thread

https://groups.google.com/forum/#!topic/circos-data-visualization/g_y2AdQuoTM

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.

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