Using Circos to connect repeat regions within a mitochondrial genome

Question

[Yongjie Zhang]

Dear All,

I am a new user of Circos and have puzzles needing your help.

I have a circular mitogenome of a fungus. Some dispersed and inverted repeat sequences are found in the mitogenome. I want to use red ribbons to connect these repetitive regions by Circos, but do not know how to prepare the conf files. Examples provided by Circos run well in my computer. I have data about start and end positions of these repeats and specific positions of each mitochondrial gene. Could you please clarify how to prepare the Circos input files? And how to make those position information into its conf file?

Other suggestions to draw the circular map and red ribbons are also highly appreciated.

Thanks very much for your help.

Sincerely,

Yongjie

Answer 1

[Ibrahim Tanyalcin]

Dear,

If you already have the start and the end positions and your karyotype file ready, than first pair them like this:

chromosome start end chromome start end

the first 3 will link to the latter 3. Save this file as links.txt etc.

Than make a conf file (just a text file) called links.conf. Within this, give path to the links.txt. Specify the parameters and the colors as shown in circos tutorials. Than if you want to change the radius1 and radius2 parameters you can define rules in a rule block within the links.conf such as:

<rules>
<rule>
condition = var(chr1) =~ /hs/
radius1 = 0.85r
radius2 = eval(...*(some code here)*)
z = eval(remap_int(var(*some parameter here*),2,8,0,10))
flow = continue
</rule>
</rules>

[Yongjie Zhang]

Thank you, Ibrahim. If I want to draw the circular mitogenome map, in which file the gene start/end position information should be put? What's the file name and the data format?

[Ibrahim Tanyalcin]

You will can them in a file called links.txt and give path to that file in the link.conf file.Your links.txt will have lines like this:

hs3 178866310 178952497 chrU 401673148 401749416 extraparameter=4,anotherextraparameter=96
.
.
.

and then in your links. conf file refer to links.txt:

file           = X:\links.txt

finally in your circos.conf include the links.conf:

<<include links.conf>>