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Create a circos plot based on 23andMe raw data

Dear community,

I got 2 data sets of raw 23andMe SNP data (.txt files) and I would like to create a circos plot with connected genes (like here). I don't really care about the meaning, or what the connection of genes is based on (in the example above it's the KEGG database), I much rather aim for a beautiful image (it's an data/art project).

I have circos installed, I converted the raw data to VCF (if needed) but I'm clueless on how to draw lines between ideograms in circos.

Any ideas are much appreciated! Thanks guys,

Dennis

snp circos 23andme vcf
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updated by cschu181 cschu181 • written by Dennis • Dennis

1 answer

To generate links you need to have your data in a tabular format (I think tab-delimited or space-delimited works). The columns are as follows.

Assuming you want to connect a region on chromosome A with a region on chromosome B and this table is in a file named linkdata.txt.

  1. ID of chromosome A
  2. start position on chromosome A
  3. end position on chromosome A
  4. ID of chromosome B
  5. start position on chromosome B
  6. end position on chromosome B

I think you can also have a 7th column with attributes for the link, such as colour etc.

Edit: Strike the previous sentence. If I understand correctly, colours and other attritbutes are set for a group of links in the <link> section described below.

Then in your circos configuration file you need to have a section named <links>, in which you reference the data file:

<links>    
<link>
file          = linkdata.txt
radius        = 1r
bezier_radius = 0r
color         = black_a4
thickness     = 2
</link>    
</links>

For more ideas, have a look at the official circos documentation for links.

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written by cschu181 cschu181

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