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>> <image> <<include etc/image.conf>> </image> karyotype = data/karyotype/karyotype.human.txt chromosomes_units = 1000000 chromosomes_display_default = no # to explicitly define what is drawn #chromosomes = hs1:0-100;hs2:50-150;hs3:50-100;hs4;hs5;hs6;hs7;hs8 # use chromosomes_breaks to indicate which regions you want to supress #chromosomes = hs1;hs2;hs3;hs4;hs5;hs6;hs7;hs8 #chromosomes_breaks = -hs1:100-200;-hs2:0-50;-hs2:150-);-hs3:0-50 # combine region declarations and breaks chromosomes = hs1:0-100;hs2:0-100;hs3:0-100;hs4:0-100;hs5;hs6;hs7;hs8 chromosomes_breaks = -hs1:25-75;-hs2:25-75;-hs3:25-75;-hs4:25-75;-hs5:75-);-hs6:0-10,75-);-hs7:75-);-hs8:75-) <<include etc/housekeeping.conf>>
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 4
<ideogram> <spacing> default = 0.005r break = 0.5r 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 = 2p </break> <break_style 2> stroke_color = black stroke_thickness = 5p thickness = 2r </break> </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = bold # labels outside circle #label_radius = dims(ideogram,radius) + 0.05r #labels inside circle label_radius = dims(ideogram,radius) - 0.15r label_with_tag = yes label_size = 48 label_parallel = yes label_case = upper
radius = 0.90r thickness = 100p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> skip_first_label = no skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 3p label_separation = 1p multiplier = 1e-6 color = black thickness = 4p size = 20p <tick> spacing = 1u show_label = no thickness = 2p color = dgrey </tick> <tick> spacing = 5u show_label = no thickness = 3p color = vdgrey </tick> <tick> spacing = 10u show_label = yes label_size = 20p label_offset = 10p format = %d grid = yes grid_color = dgrey grid_thickness = 1p grid_start = 0.5r grid_end = 0.999r </tick> </ticks>