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 # use this to see how relative ticks can be drawn relative to # the ideograms (use rdivisor=ideogram in the tick blocks) #chromosomes = hs1[a]:0-75;hs1[b]:100-150;hs1[c]:200-) chromosomes = hs1 chromosomes_display_default = no <<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>> radius* = 0.75r </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> radius = dims(ideogram,radius_outer) multiplier = 1/1u color = black force_display = yes thickness = 2p show_label = yes format = %d size = 20p thicknes = 4p label_offset = 5p <tick> show = yes spacing = 1u rspacing = 0.02 # this is the default spacing type spacing_type = absolute label_size = 24p </tick> <tick> # when spacing_type is relative, define # rspacing to be the increment show = yes rspacing = 0.01 spacing_type = relative color = red label_size = 30p offset = 85p label_relative = yes rmultiplier = 100 suffix = % # This will make ticks spaced relatively by ideogram, # and not chromosome. This setting is useful when # the chromosome is displayed as multiple ideograms # rdivisor = ideogram </tick> <tick> show = yes rspacing = 0.1 spacing_type = relative thickness = 3p color = blue label_size = 36p offset = 215p label_relative = yes rmultiplier = 10 suffix = /10 #rdivisor = ideogram </tick> </ticks>