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 = hs9[a]:40-45;hs1[b]:40-45;hs9[c]:65-70;hs1[d]:50-55 chromosomes_display_default = no <plots> type = tile layers_overflow = hide <plot> file = data/6/assembly.txt r1 = 0.98r r0 = 0.86r orientation = out layers = 15 margin = 0.02u thickness = 15 padding = 8 stroke_thickness = 1 stroke_color = grey </plot> <plot> file = data/6/genes.txt r1 = 0.84r r0 = 0.71r orientation = center layers = 11 margin = 0.02u thickness = 8 padding = 4 layers_overflow = collapse layers_overflow_color = red stroke_thickness = 1 stroke_color = dgreen color = green <backgrounds> <background> color = vvlgrey </background> </backgrounds> </plot> <plot> file = data/6/variation.txt r1 = 0.69r r0 = 0.5r orientation = in layers = 15 margin = 0.02u thickness = 10 padding = 5 stroke_thickness = 1 stroke_color = dblue color = blue </plot> <plot> file = data/6/segdup.txt r1 = 0.525r r0 = 0.2r orientation = in layers = 15 margin = 0.02u thickness = 8 padding = 5 layers_overflow = hide color = orange <backgrounds> color = vlgrey_a5 <background> y1 = 0.25r </background> <background> y1 = 0.5r </background> <background> y1 = 0.75r </background> <background> y1 = 1r </background> </backgrounds> <rules> <rule> condition = var(size) < 150kb color = eval((qw(lgrey grey dgrey vdgrey black))[remap_round(var(size),10000,150000,0,4)]) </rule> </rules> </plot> <plot> file = data/6/conservation.txt r0 = 0.2r r1 = 0.525r orientation = out layers = 5 margin = 0.02u thickness = 8 padding = 5 layers_overflow = grow layers_overflow_color = red color = lpurple <rules> <rule> condition = ! on(hs1) color = blue stroke_thickness = 1 stroke_color = dblue </rule> </rules> </plot> </plots> <<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>> 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 <tick> spacing = .1u show_label = no </tick> <tick> spacing = .5u show_label = yes label_size = 20p format = %d </tick> <tick> spacing = 1u show_label = yes label_size = 24p format = %d </tick> </ticks>