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>> karyotype = data/karyotype/karyotype.human.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes_display_default = yes <links> <link> file = data/8/11/links.withvalue.txt ribbon = yes flat = yes radius = 0.95r bezier_radius = 0r crest = 0.2 <rules> <rule> # always trigger this rule condition = 1 # use the link's value to sample from a list of colors color = eval((qw(red orange green blue purple))[ var(value) ]) # continue parsing other rules flow = continue </rule> <rule> # always trigger this rule condition = 1 # add _a3 to the color of the ribbon, giving it 50% transparency (3/6) color = eval(sprintf("%s_a3",var(color))) </rule> </rules> </link> </links> <<include etc/housekeeping.conf>>
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 3
<ideogram> <spacing> default = 0.005r break = 0.5r axis_break_at_edge = yes axis_break = yes axis_break_style = 2 <break_style 1> stroke_color = black fill_color = blue thickness = 0.25r stroke_thickness = 2 </break> <break_style 2> stroke_color = black stroke_thickness = 2 thickness = 1.5r </break> </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius) - 50p label_size = 36 label_parallel = yes label_case = lower label_format = eval(sprintf("chr%s",var(label)))
radius = 0.85r thickness = 30p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> tick_separation = 3p label_separation = 5p radius = dims(ideogram,radius_outer)+50p multiplier = 1e-6 color = black size = 20p thickness = 4p label_offset = 5p format = %d <tick> spacing = 1u show_label = yes label_size = 16p </tick> <tick> spacing = 5u show_label = yes label_size = 18p </tick> <tick> spacing = 10u show_label = yes label_size = 20p </tick> <tick> spacing = 20u show_label = yes label_size = 24p </tick> </ticks>