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;hs2;hs3 chromosomes_display_default = no # If you adjust the radius of the ideograms, links incident # on these ideograms will inherit the new radius. #chromosomes_radius = hs2:0.9r;hs3:0.8r # Links (bezier curves or straight lines) are defined in <links> blocks. # Each link data set is defined within a <link> block. # # As with highlights, parameters defined # in the root of <links> affect all data sets and are considered # global settings. Individual parameters value can be refined by # values defined within <link> blocks, or additionally on each # data line within the input file. <links> <link> file = data/5/segdup.txt radius = 0.95r color = black_a4 # Curves look best when this value is small (e.g. 0.1r or 0r) bezier_radius = 0.1r thickness = 1 # These parameters have default values. To unset them # use 'undef' #crest = undef #bezier_radius_purity = undef # Limit how many links to read from file and draw record_limit = 2000 </link> </links> <<include etc/housekeeping.conf>> data_out_of_range* = trim # If you want to turn off all track default values, # uncomment the line below. This overrides the # value of the parameter imported from etc/housekeeping.conf #track_defaults* = undef # The defaults for links are # # ribbon = no # color = black # thickness = 1 # radius = 0.40r # bezier_radius = 0r # crest = 0.5 # bezier_radius_purity = 0.75 # # See etc/tracks/link.conf in Circos distribution
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>