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;hs2;hs3;hs4 <links> z = 0 radius = 0.975r crest = 1 color = vlgrey bezier_radius = 0r bezier_radius_purity = 0.5 thickness = 2 <link> file = data/5/segdup.txt <rules> <rule> # multiple conditions are combined with AND # i.e. all conditions must be satisfied condition = var(interchr) condition = within(hs2,40Mb,80Mb) z = 60 color = red thickness = 5 </rule> <rule> condition = max(var(size1),var(size2)) > 40kb z = 50 color = green thickness = 5 </rule> <rule> condition = max(var(size1),var(size2)) > 10kb z = 45 color = dgrey thickness = 4 </rule> <rule> condition = max(var(size1),var(size2)) > 5kb z = 40 color = grey thickness = 3 </rule> <rule> condition = max(var(size1),var(size2)) > 1000 z = 35 color = lgrey thickness = 2 </rule> </rules> </link> </links> <<include etc/housekeeping.conf>> data_out_of_range* = trim
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 0
<ideogram> <spacing> default = 0.01r break = 0.5r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(ideogram,radius) + 0.075r label_with_tag = yes label_size = 36 label_parallel = yes label_case = lower label_format = eval(sprintf("chr%s",var(label)))
radius = 0.90r thickness = 100p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> radius = dims(ideogram,radius_outer) orientation = out label_multiplier = 1e-6 color = black size = 20p thickness = 3p label_offset = 5p <tick> spacing = 1u show_label = no </tick> <tick> spacing = 5u show_label = yes label_size = 20p format = %d </tick> <tick> spacing = 10u show_label = yes label_size = 24p format = %d </tick> </ticks>