Need help explaining the output of link files generated using SVDetect

[anibhax]

Hi,

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 the 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 I also noticed that only about 8 colors are present.

Any help making me understand this output is appreciated. I have looked everywhere, but I never any page explaining these colors.

Thanks!

[TiborNagy]

The first column is the link ID. So two line identify one connection between two positions. The reason behind this is the flexibility. You can create a link between three or more position. The color is simply the color of the connection line in the final image. Circos has a very few default values, so you need to define every parameter.

[anibhax]

Can you elaborate on that? The first two rows have the same id's: 1. So I'm assuming this means that links exist between chr1 and chr18. Does this mean it is a inter-chromosomal link? And do you know from which position to which position the link is drawn in this case?

Thanks!

[TiborNagy]

Yes, the first two rows are an interchromosomal link. The positions can be found in the 3th and 4th columns. Actually it is not a single position, but a region.

[anibhax]

That makes sense. Thanks!