Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
Circos draws links without orientation. To indicate the direction of the link, you need to compose the link track with another track, which will provide an indication of which end of the link is its end (or start, if you wish).
To do so, the best way is to use a scatter plot with a triangular glyph. The glyph will act as a natural arrowhead at the end of the link.
To prepare your data, create a scatter plot data file that contains the coordinates of the ends of the links. For example, if your links are
hs1 102024400 102025440 hs3 111883743 111884767 hs1 152617218 152618252 hs3 111883745 111884756 hs1 158502674 158503718 hs3 111883744 111884768 ...
the list of ends might be
hs1 102024400 102025440 0 hs1 152617218 152618252 0 hs1 158502674 158503718 0 ...
I've selected the second coordinate of the link as its end (arbitrarily, for this example), and set the y-value of the associated data point to 0.
The scatter track that adds the arrow head would be defined like this
<plots> <plot> type = scatter file = linkends.txt glyph = triangle glyph_size = 24p min = 0 max = 1 r0 = 0.99r r1 = 0.99r fill_color = black <rules> <rule> condition = 1 fill_color = eval(lc "chr".substr(var(chr),2)) </rule> </rules> </plot> </plots>
I've added a rule that colors the glyph by the color of the chromosome on which it lies.
The scatter plot is placed at
radius=0.99r, which is just before where the links end, to seamlessly join the triangular glyphs to the link line.
You can use other tracks to indicate the end of the link, such as a highlight track, to give the link a thicker base, or a text track (to give the end of the link a name).