How to use circos to display gene duplications in a genome.

[Nikii Frey]

Kindly guide me on how to use circos to get a display like  one below.I have also attached a snapshot of my data.

Basically i want a image which will display various duplication across different chromosomes in a genome.

I have successfull installled circos and read the documentation but i cannt figure out how to go about...i wanna know how to generate the input files give that my data is as attached .

[Martin Krzywinski]

This is covered in the links tutorial.

http://www.circos.ca/documentation/tutorials/links/basic_links/

Each duplication would be a link, represented by a line like

hs10 4262515 4262515 hs10 11529039 11529039 

This assumes that you only have a point coordinates for the duplication. If you have a start/end position on each chromosome, then you'd use those as the coordinate.

Note that conventionally Circos uses "hs" prefix for human chromosomes, not "chr". This is reflected in the names of the chromosomes as defined in the human karyotype.

You can optionally add the score and type

hs10 4262515 4262515 hs10 11529039 11529039 score=1e-22,type=segmental

for use in rules.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[chebii vivien]

Thanks Martin for the information.Let me try to   work on  it.

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[chebii vivien]

Thanks Martin for the information.Let me try to   work on  it.

On Wed, Jul 30, 2014 at 3:18 AM, Martin Krzywinski <martin.k...@gmail.com> wrote:

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[chebii vivien]

Hi Martin,

Iam stuck again,kindly help...when i run circos i get following error message

 *** CIRCOS ERROR ***

  You tried to test the number [43,267,665] with a number regular expression of

  type [int] but this type is not defined. Regexp::Common module returned error

  [ at /home/vivienne/circos-0.66/bin/../lib/Circos/Error.pm line 362

      Circos::Error::fatal_error('parsedata', 'bad_number', '43,267,665', 'int')

      called at /home/vivienne/circos-0.66/bin/../lib/Circos/Utils.pm line 329

      eval {...} called at /home/vivienne/circos-0.66/bin/../lib/Circos/Utils.pm

      line 326

      Circos::Utils::is_number('43,267,665', 'int') called at

      /home/vivienne/circos-0.66/bin/../lib/Circos/Karyotype.pm line 132

      Circos::Karyotype::read_karyotype_file('vivien/etc/karyotype.txt',

      'HASH(0x30f5d10)') called at

      /home/vivienne/circos-0.66/bin/../lib/Circos/Karyotype.pm line 94

      Circos::Karyotype::read_karyotype('file', 'vivien/etc/karyotype.txt')

      called at /home/vivienne/circos-0.66/bin/../lib/Circos.pm line 274

      Circos::run('Circos', 'configfile', 'etc/circos.conf') called at

      ../bin/circos line 300

Attached is  the  datasets .

i made the karyotype file using the data  provided in the   MSU rice genome database(the data in gff3 file format)

Thanks .

[Martin Krzywinski]

Your chromosome ends in karyotype.txt have a , thousands separator. Remove this.

Also, each chromosome should start at 0. In principle you can use a non-zero start, but this isn't well tested. If you want to avoid drawing regions, crop them out with the 'chromosomes_breaks' parameter

http://www.circos.ca/documentation/tutorials/ideograms/cropping/

...

chr - Os9 9 2874  23,011,485 black

chr - Os10 10 3710 23,206,044 black

chr - Os11 11 1162 29,014,744 black

chr - Os12 12 2682 27,529,682 black

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca