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>> show_ticks* = no karyotype = data/karyotype/karyotype.human.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes = hs1 chromosomes_display_default = no <plots> type = text color = black label_font = default label_size = 24p <plot> file = data/6/text.genes.txt r1 = 1r+200p r0 = 1r show_links = yes link_dims = 0p,0p,70p,0p,10p link_thickness = 2p link_color = red </plot> <plot> file = data/6/text.genes.znf.txt r1 = 0.8r r0 = 0.4r show_links = yes link_dims = 4p,4p,8p,4p,4p link_thickness = 2p link_color = red </plot> </plots> <<include etc/housekeeping.conf>>
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>> radius* = 0.825r </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius)-30p label_size = 24 label_parallel = yes label_case = lower label_format = eval(sprintf("chr%s",var(label)))
radius = 0.775r thickness = 30p 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 format = %d <tick> spacing = 1u show_label = no size = 10p </tick> <tick> spacing = 5u show_label = yes label_size = 20p size = 15p </tick> <tick> spacing = 10u show_label = yes label_size = 24p </tick> </ticks>