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.
<colors> <<include etc/colors.conf>> </colors> <fonts> <<include etc/fonts.conf>> </fonts> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/karyotype.human.txt <image> dir = /tmp file = circos-tutorial.png # radius of inscribed circle in image radius = 1500p background = white # by default angle=0 is at 3 o'clock position angle_offset = -90 </image> 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 anglestep = 0.5 minslicestep = 10 beziersamples = 40 debug = no warnings = no imagemap = no # don't touch! units_ok = bupr units_nounit = n svg_font_scale = 1.3
<ideogram> <spacing> default = 3u break = 1u </spacing> # thickness (px) of chromosome ideogram thickness = 100p stroke_thickness = 2 # ideogram border color stroke_color = black fill = yes # the default chromosome color is set here and any value # defined in the karyotype file overrides it fill_color = black # fractional radius position of chromosome ideogram within image radius = 0.75r show_label = no label_with_tag = yes label_font = condensedbold label_radius = dims(ideogram,radius_outer) + 0.075r label_size = 48p # cytogenetic bands band_stroke_thickness = 2 # show_bands determines whether the outline of cytogenetic bands # will be seen show_bands = yes # in order to fill the bands with the color defined in the karyotype # file you must set fill_bands fill_bands = yes </ideogram>
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 <tick> show = yes spacing = 1u rspacing = 0.02 # this is the default spacing type spacing_type = absolute size = 8p label_size = 24p offset = 10p </tick> <tick> # when spacing_type is relative, define # rspacing to be the increment show = yes rspacing = 0.01 spacing_type = relative size = 8p color = red label_size = 36p offset = 80p 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 size = 12p thickness = 3p color = blue label_size = 36p offset = 210p label_relative = yes rmultiplier = 10 suffix = /10 #rdivisor = ideogram </tick> </ticks>