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.
In previous tutorials, tick marks have been formatted by a combination of the multiplier and format parameters. The multiplier served to derive a value for the tick label (value = position * multiplier) and the format string controlled how the value was shown.
For example, if multiplier = 1/1u (it can be expressed in units of chromosomes_units; e.g., 1/1u = 1e-6 if chromosomes_units = 1000000) and format %d, then the tick mark at 10,000,000 will be labeled 10. If format is %.2f, then the label will be 10.00.
The multiplier is useful to avoid the presence of large number of non-significant zeroes in the labels. You can change the format for each <tick> block. For example, with a multiplier of 1/1u, the ticks spaced every 1 Mb should have a format of %d, whereas ticks spaced every 0.1 Mb should receive a format of %.1f. Note that there is no relation between the "multiplier" and "chromosomes_unit" parameters.
<ticks> multiplier = 1/1u ... <tick> format = %d ... </tick> <tick> format = %.1f ... </tick> ... </ticks>
You can adjust the multipler for each tick level. For example, the second tick level in the configuration below uses a 1000/1u multiplier instead of 1/1u. This would result in a label "100000" (or "100,000" if thousands_sep=yes) instead of "100".
<ticks> multiplier = 1/1u ... <tick> ... </tick> <tick> multiplier = 1000/1u thousands_sep = yes ... </tick> ... </ticks>
If defined, the value of "mod" is used to adjust the label by performing modulo arithmetic on the tick mark value based on the formula.
given mod = M then tick_label = mod(tick_value,M) * multiplier
The "mod" parameter is expected to be defined locally within each <tick> block. Its purpose is to further reduce the complexity of the tick labels for finer ticks. For example, if you have ticks every 1u and every 0.1u (e.g., u = 1,000,000) and set
multiplier = 1/1u <tick> spacing = 0.1u mod = 1u </tick>
Then the label at tick mark 10,100,000 would be
mod(10,100,000 , 1,000,000) * 1e-6 = 100,000 * 1e-6 = 0.1
rather than 10.1. If you redefine the multiplier for this tick block to 10/1u, then your ticks would progress as follows
0 1 2 ... 8 9 10 1 2 ... 8 9 20 1 2 ... 8 9 30 1 2 ...
You should always define your tick mark parameters in units of "u" (the value of the chromosomes_units parameter). Doing so will give the context of your configuration file the same length scale as your ideograms (e.g. mammalian genome images might use 1u=1000000 whereas smaller genomes might use 1u=1000).
You can additionally alter the tick mark label with a suffix and prefix by defining a "suffix" and "prefix" parameters.
... <tick> suffix = kb prefix = + ... </tick>
You can also add a prefix or suffix by adjusting the format of the tick.
<tick> format = position %.1f kb ... </tick>