How to perform mutiple genomes with circos?

Question

[2351688559]

I want to use circos to show 4 bacterial genomes, with one track representing one genome. I 've seen the examples given in the tutorials of showing mutiple genomic data, but it seems that all genomes were shown in a single track. That is not I want. Would anyone provide a hint? Thanks!

[Michael]

Do you want to make synteny plots like this? Then you should think this approach over, because it will become a very confusing and chaotic plot. There is a reason why the plots you have seen use a single track.

Answer 1

[Ibrahim Tanyalcin]

Dear 2351688559,

Basic circos plot file has the format chr start end value (or name chr start end value). Then when you have 1 genome you have chr1, chr2 .... chr X etc. Then if you have 4 genomes, just change the chr names adding abbreviation. For example think of a datatrack file like below:

chr1 123 123124 value
chr1 123 123145 value
...
...
chr1_G2 123 1234 value
chr1_G2 123 123124 value
...
...
chr1_G3 123 123144 value
chr1_G3 12314 123124 value
...

Than in the configuration file ideogram.conf, increase the space between ideograms with different _G (chrLast_G1;chr1_G2 etc) extension using the <pairwise> block within the <spacing> block of your conf file.

Hope it helps, Good luck,

[2351688559]

Well, looks like all the genomes are still in a single track, but actually it is also a good way to show mutiple genomes wirhin the figure. Thank you very much for providing sunch detailed solution! Although I still do not want to give up considering showing the genomes in different tracks.

[Ibrahim Tanyalcin]

Dear,

In that case, you have a second option. Here is the idea:

First render a mock karyotype which is longer than the sum of all genomes you want to render. For example lets say you have 3 genomes, 1Gb, 2Gb and 3Gb. Now make a karyotype that is 9Gb long, 6Gb of it will be used for real genomes and 1gb for space between. Now do not render the karyotype, show it as a transparent line or a line with 0 thickness. Next,render your genomes and all related information as highlights. So you will have 3 highlights block plus any additional highlights that you wanna render, render over them with higher z index.

I hope it helps,