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 <links> z = 0 radius = 0.975r crest = 0.5 bezier_radius = 0.5r bezier_radius_purity = 0.75 <link> z = 50 color = green_a2 thickness = 4 file = data/5/segdup.bundle3.txt bezier_radius_purity = 0.2 crest = 1 </link> <link> z = 40 color = orange_a2 thickness = 4 file = data/5/segdup.bundle2.txt bezier_radius_purity = 0.2 crest = 1 </link> <link> z = 30 color = blue_a2 thickness = 4 file = data/5/segdup.bundle1.txt bezier_radius_purity = 0.2 crest = 1 </link> <link> z = 20 color = dgrey_a2 thickness = 3 file = data/5/segdup.txt record_limit = 500 </link> <link> z = 15 color = grey_a2 thickness = 3 file = data/5/segdup.txt record_limit = 1000 </link> <link> z = 10 color = lgrey_a2 thickness = 2 file = data/5/segdup.txt record_limit = 2500 </link> <link> z = 5 color = vlgrey_a2 thickness = 1 file = data/5/segdup.txt record_limit = 10000 </link> </links> <<include etc/housekeeping.conf>> data_out_of_range* = trim
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 0
<ideogram> <spacing> default = 0.01r break = 0.5r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(ideogram,radius) + 0.075r label_with_tag = yes label_size = 36 label_parallel = yes label_case = lower label_format = eval(sprintf("chr%s",var(label)))
radius = 0.90r thickness = 100p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> radius = dims(ideogram,radius_outer) orientation = out label_multiplier = 1e-6 color = black size = 20p thickness = 3p label_offset = 5p <tick> spacing = 1u show_label = no </tick> <tick> spacing = 5u show_label = yes label_size = 20p format = %d </tick> <tick> spacing = 10u show_label = yes label_size = 24p format = %d </tick> </ticks>