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.
<<include etc/colors_fonts_patterns.conf>> <colors> rep = 211,121,111 dem = 85,143,190 </colors> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> chromosomes_units = 1 chromosomes_display_default = yes karyotype = karyotype.txt <links> <link> file = links.txt radius = dims(ideogram,radius_inner) bezier_radius = 0r thickness = 5 color = rep # make it republican, by default <rules> <rule> # set dem color if start is on a democrat condition = var(chr1) =~ /obama|richardson|clinton/ color = dem </rule> </rules> </link> </links> <plots> <plot> file = slices.txt type = highlight r0 = dims(ideogram,radius_inner) r1 = dims(ideogram,radius_outer) fill_color = undef stroke_color = white stroke_thickness = 5 </plot> <plot> z = 10 type = highlight file = axis.txt r0 = dims(ideogram,radius_outer) - 2p r1 = dims(ideogram,radius_outer) + 3p fill_color = black </plot> </plots> <<include etc/housekeeping.conf>> track_defaults* = undef
<ideogram> <spacing> default = 0.01r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius)-70p label_with_tag = yes label_size = 40 label_parallel = yes label_case = upper
radius = 0.90r thickness = 150p fill = yes
show_ticks = yes show_tick_labels = yes <ticks> radius = dims(ideogram,radius_outer) multiplier = 1 color = black thickness = 4p size = 20p <tick> spacing = 100u </tick> </ticks>