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;hs3:0-100 chromosomes = hs1 #chromosomes_scale = hs1:0.5;hs2:1;hs3:6.5 <zooms> <zoom> chr = hs1 start = 100u end = 110u scale = 10 smooth_steps = 10 smooth_distance = 5r </zoom> </zooms> <<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>> </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 = 1e-6 label_offset = 5p thickness = 4p size = 20p # ticks must be separated by 10 pixels in order to be displayed tick_separation = 15p <tick> spacing = 0.25u color = red show_label = no label_size = 12p format = %.2f </tick> <tick> spacing = 0.5u color = blue show_label = no label_size = 12p format = %.2f </tick> <tick> spacing = 1u color = green show_label = no label_size = 12p format = %.2f </tick> <tick> spacing = 5u color = black show_label = yes label_size = 20p format = %d </tick> <tick> spacing = 10u color = black show_label = yes label_size = 24p format = %d </tick> </ticks>