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>> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt,data/karyotype/karyotype.rat.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes_display_default = no chromosomes = hs1;hs2;hs3;/mm1[4-9]/ #chromosomes_scale = /hs/:0.25r #chromosomes_scale = /mm/:0.0833r # if 6 mouse ideograms are drawn, these two chromosomes_scale = /mm/:0.5rn # are equivalent #chromosomes_display_default = yes #chromosomes_scale = /hs/:0.25r #chromosomes_scale = /mm/:0.0833r # if 6 mouse ideograms are drawn, these two #chromosomes_scale = /mm/:0.5rn # are equivalent #chromosomes_color = /hs/:green;/mm/:red;/rn/:blue #chromosomes_scale = /mm/:0.175rn;/rn/:0.2rn <<include etc/housekeeping.conf>>
show_bands = no fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 3
axis_break_at_edge = yes axis_break = yes axis_break_style = 2 <break_style 1> stroke_color = black fill_color = blue thickness = 0.25r stroke_thickness = 2 </break_style> <break_style 2> stroke_color = black stroke_thickness = 2 thickness = 2r </break_style>
<ideogram> <spacing> default = 0.0025r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius) - 50p label_size = 18 label_parallel = yes label_case = lower label_format = eval(var(chr))
radius = 0.90r thickness = 50p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> tick_separation = 3p label_separation = 5p radius = dims(ideogram,radius_outer) multiplier = 1e-6 color = black thickness = 2p label_offset = 5p format = %d <tick> spacing = 0.5u show_label = no size = 6p </tick> <tick> spacing = 1u show_label = yes label_size = 16p size = 10p </tick> <tick> spacing = 5u show_label = yes label_size = 18p size = 14p </tick> <tick> spacing = 10u show_label = yes label_size = 20p size = 18p </tick> <tick> spacing = 20u show_label = yes label_size = 24p size = 22p </tick> <tick> spacing = 50u show_label = yes label_size = 24p size = 22p </tick> </ticks>