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.
<colors> <<include etc/colors.conf>> </colors> <fonts> <<include etc/fonts.conf>> </fonts> <<include ideogram.conf>> <<include ticks.conf>> karyotype = karyotype.human.hg18.txt <image> dir = . file = links-directed.png 24bit = yes radius = 1500p background = white angle_offset = -90 auto_alpha_colors = yes auto_alpha_steps = 5 </image> chromosomes_units = 1e6 chromosomes_display_default = yes chromosomes = hs3:101-121 chromosomes_scale = hs3:50 <plots> <plot> type = scatter glyph = triangle glyph_size = 24p file = linkends.txt min = 0 max = 1 r0 = 0.99r r1 = 0.99r fill_color=black <rules> <rule> importance = 100 condition = 1 fill_color = eval("chr".substr(_CHR_,2)) </rule> </rules> </plot> </plots> <links> <link testlinks> file = links.txt thickness = 2 bezier_radius = 0r radius = 0.995r crest = 0.25 color = black_a2 </link> </links> anglestep = 0.5 minslicestep = 10 beziersamples = 120 debug = no warnings = no imagemap = no units_ok = bupr units_nounit = n #debug_group = ticks
<ideogram> <spacing> default = 5u </spacing> # thickness (px) of chromosome ideogram thickness = 20p 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 = 0.85r show_label = no label_font = condensedbold label_radius = dims(ideogram,radius) + 0.10r label_size = 36 label_parallel = no # cytogenetic bands band_stroke_thickness = 2 # show_bands determines whether the outline of cytogenetic bands # will be seen show_bands = no # in order to fill the bands with the color defined in the karyotype # file you must set fill_bands fill_bands = no band_transparency = 1 </ideogram>
show_ticks = yes show_tick_labels = yes grid_start = dims(ideogram,radius_inner)-0.5r grid_end = dims(ideogram,radius_outer)+100 <ticks> skip_first_label = no skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 5p min_label_distance_to_edge = 0p label_separation = 5p label_offset = 5p label_size = 8p multiplier = 1e-6 color = black <tick> spacing = 5u size = 8p thickness = 2p color = black show_label = yes label_size = 24p label_offset = 0p format = %d grid = yes grid_color = grey grid_thickness = 1p </tick> <tick> #chromosomes_display_default=no #chromosomes = hs3 spacing = 1u size = 8p thickness = 2p color = black show_label = yes label_size = 24p label_offset = 0p format = %d grid = yes grid_color = grey grid_thickness = 1p </tick> <tick> spacing = 25u size = 12p thickness = 2p color = black show_label = yes label_size = 24p label_offset = 0p format = %d grid = yes grid_color = dgrey grid_thickness = 1p </tick> </ticks>