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 = hs1[a]:0-75;hs1[b]:100-150;hs1[c]:200-) chromosomes = hs1 chromosomes_display_default = no <<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> label_separation = 5p radius = dims(ideogram,radius_outer) multiplier = 1/1u color = black thickness = 4p show_label = yes label_offset = 5p format = %d size = 20p <tick> spacing = 1u radius = dims(ideogram,radius_outer) label_size = 18p format = %d color = purple </tick> <tick> spacing = 2.5u radius = 0.8r label_size = 36p format = %.1f color = green </tick> <tick> spacing = 5u radius = dims(ideogram,radius_outer) radius = 0.8r radius = 0.4r label_size = 36p </tick> <tick> spacing = 10u radius = dims(ideogram,radius_outer) radius = 0.8r radius = 0.4r radius = 0.25r show = yes label_size = 36p color = red </tick> <tick> spacing = 50u radius = dims(ideogram,radius_outer) radius = 0.8r radius = 0.4r radius = 0.25r radius = 0.1r label_size = 36p color = blue </tick> </ticks>