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>> karyotype = data/karyotype/karyotype.human.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000 chromosomes = hs1:0-1 chromosomes_display_default = no <plots> type = text color = black label_font = mono label_size = 32 show_links = no rpadding = 0.2r <plot> file = data/6/sequence.txt r1 = 0.9r r0 = 0.3r label_size = 16 padding = -0.25r <rules> <<include rule.textcolor.conf>> </rules> </plot> <plot> file = data/6/sequence.txt r1 = 0.9r r0 = 0.4r rpadding = 0.25r <rules> <<include rule.textcolor.conf>> </rules> </plot> <plot> file = data/6/sequence.long.txt r1 = 0.9r r0 = 0.7r label_rotate = no <rules> <<include rule.textcolor.conf>> </rules> </plot> <plot> file = data/6/sequence.txt r0 = 1r+80p r1 = 1r+250p label_parallel = yes <rules> <rule> condition = var(value) ne "A" show = no </rule> <rule> condition = 1 label_size = eval(12+32*rand()) </rule> </rules> </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
<rule> condition = var(value) eq "A" color = red </rule> <rule> condition = var(value) eq "T" color = blue </rule> <rule> condition = var(value) eq "C" color = green </rule>
show_ticks = yes show_tick_labels = yes show_grid = no grid_start = dims(ideogram,radius_inner)-0.5r grid_end = dims(ideogram,radius_inner) <ticks> radius = dims(ideogram,radius_outer) label_offset = 5p label_size = 20p multiplier = 1 color = black format = %d size = 10p thickness = 2p <tick> spacing = 0.002u show_label = no </tick> <tick> spacing = .02u show_label = yes </tick> <tick> spacing = .1u show_label = yes label_size = 24p </tick> </ticks>