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 colors_fonts_patterns.conf>> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> karyotype = data/karyotype/karyotype.human.txt chromosomes_units = 1000000 chromosomes_display_default = no chromosomes = hs1:0-100 <<include etc/housekeeping.conf>>
show_bands = no fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 0
<ideogram> <spacing> default = 0.01r break = 2u </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = (dims(ideogram,radius_inner) + dims(ideogram,radius_outer))/2 label_center = yes label_size = 72 label_with_tag = yes label_parallel = yes label_case = upper
radius = 0.90r thickness = 100p fill = no fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> # global offset for ticks (remember that labels are automatically offset) offset = 0p radius = dims(ideogram,radius_outer) multiplier = 1e-6 thickness = 4p # if set to yes, all ticks at all spacings will be drawn, regardless of whether # there is another tick at this position (e.g. at 100Mb the ticks for 10u, 5u and 1u # will be drawn. force_display=yes is useful only when offset is used to make each # tick set drawn at a different radial position) force_display = no # global label offset - useful if set to relative size # (will be relative to ticks size) # local label offsets add to this value # label_offset = 0.5r <tick> spacing = 0.5u offset = 0p size = 15p color = red show_label = yes label_size = 20p label_offset = dims(tick,max_tick_length) - 15p format = %.1f </tick> <tick> spacing = 1u offset = 0p size = 20p color = blue show_label = yes label_size = 20p label_offset = dims(tick,max_tick_length) - 20p format = %d </tick> <tick> spacing = 5u offset = 0p size = 25p color = green show_label = yes label_size = 20p label_offset = dims(tick,max_tick_length) - 25p format = %d </tick> <tick> spacing = 10u offset = 0p size = 30p color = black show_label = yes label_size = 24p label_offset = dims(tick,max_tick_length) - 30p format = %d </tick> </ticks>