I have used
SVDetect to generate links. And I got it converted to circos input format (
segdup.txt). I don't understand the logic of this format. Here are first few lines:
1 hschr1 10000005 10000080 color=white 1 hschr18 54254700 54254735 color=white 2 hschr1 10000008 10000083 color=white 2 hschr18 19966691 19966726 color=white 3 hschr1 10000016 10000051 color=white 3 hschr16 66915746 66915821 color=white 4 hschr1 10000016 10000051 color=grey 4 hschr17 29951284 29951359 color=grey 5 hschr1 10000016 10000051 color=white 5 hschrX 15854763 15854838 color=white
Why is the color important? I understand it has something to do with generating
circos plots. Nothing more.
And without much knowledge, I tried generating
circos plots anyways, to see how the output looks like. Surprisingly there are no links in it.
SVDetect gave an example with the old version of circos plots. The circos conf format has changed quite a bit with the new one and I have modified everything to work in the current format. Just when I thought everything works fine, there are no links generated.
Here is a part of the (now updated it to the entire link section) link section in circos conf file (after my modification looking at the tutorial):
<link> show = yes color = vvdgrey thickness = 2 file = sample.ab.bam.links.compared.segdup.txt #record_limit = 2500 <rules> <rule> importance = 10 condition = var(color) eq "red" thickness = 3 z = 10 </rule> <rule> importance = 9 condition = var(color) eq "orange" thickness = 3 z = 9 </rule> <rule> importance = 8 condition = var(color) eq "purple" thickness = 3 z = 8 </rule> <rule> importance = 7 condition = var(color) eq "green" thickness = 3 z = 7 </rule> <rule> importance = 6 condition = var(color) eq "blue" thickness = 3 z = 6 </rule> <rule> importance = 5 condition = var(color) eq "black" thickness = 3 z = 5 </rule> 85 <rule> #show = no importance = 4 condition = var(color) eq "grey" thickness = 2 z = 4 </rule> </rules> </link> </links>
I only modified the condition in original conf file provided by SVDetect, which looked like this:
condition = _COLOR1_ eq "red"
Of course I have tried using the original conf file as well, but still it gave me the same image.
To summarize, if anyone can explain the format of the segdup file and how to generate links properly using circos plot I would really appreciate it.