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.
Up to now, each tick block defined a tick series, with the positions of ticks in a series defined by the spacing (absolute or relative). In this tutorial, you'll see how to define ticks at specific positions.
To define a tick at a given absolute position, use
position instead of
<ticks> ... <tick> # define position position = 25u # no spacing definition necessary ... </tick> <tick> # define multiple positions position = 30u,32u,34u,40u ... </tick> ... </ticks>
Do not define
position is used.
To place at specific relative positions, use
rposition and set
<tick> # define multiple positions rposition = 0.5,0.7,0.9 spacing_type = relative color = blue label_relative = yes format = %.2f </tick>
Note the difference between
position (for absolute positions) and
rposition (for relative positions).
Do not define
rposition is used.
Two special positions are defined. These are
end. Using these strings you can place a tick at the start or end of
the ideogram. This tick can have a label. In addition, you can define
the label to be any string by using the
label parameter. This
parameter is supported for all ticks, but is particularly useful for start/end ideogram ticks.
<tick> position = start label = 3' ... </tick> <tick> position = end label = 5' ... </tick>