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 chromosomes = hs1;hs2;hs3;hs4;hs5 <<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> #chromosomes_display_default = yes chromosomes_display_default = no # no ticks on chromosomes hs1 and hs2 # use with chromosomes_display_default = yes # chromosomes = -hs1;-hs2:0-100;-hs3:100-) chromosomes = hs1;hs2:0-100;hs3:100-) radius = dims(ideogram,radius_outer) label_offset = 5p orientation = out label_multiplier = 1e-6 color = black <tick> #chromosomes = -hs2 spacing = 1u size = 8p thickness = 2p color = dgrey show_label = no </tick> <tick> chromosomes = hs4 spacing = 5u size = 12p color = dred thickness = 2p show_label = yes label_size = 20p label_color = dred label_offset = 3p format = %d </tick> <tick> chromosomes = -hs2;hs5 spacing = 10u size = 14p thickness = 2p show_label = yes label_size = 24p label_offset = 5p format = %d </tick> </ticks>