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>> <ideogram> radius* = 0.8r </ideogram> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/karyotype/karyotype.human.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes_display_default = no chromosomes = hs1;hs2 #chromosomes = hs1[a]:0-0.8;hs1[b]:16.6-17.2;hs1[c]:141.5-148;hs1[d]:220.6-222.4;hs2[e]:90.8-95.2;hs2[f]:132.3-132.8;hs2[g]:242.5-) #chromosomes_breaks = -hs1:142.3-143.9;-hs1:144.2-144.7;-hs1:145-146;-hs1:220.8-222;-hs2:91.8-94.6 <zooms> smooth_distance = 1r smooth_steps = 40 <zoom> chr = hs1 start = 0u end = 0.5u scale = 120 </zoom> <zoom> chr = hs1 start = 16.7u end = 17u scale = 200 </zoom> <zoom> chr = hs1 start = 20u end = 100u scale = 0.1 </zoom> <zoom> chr = hs1 start = 144u end = 145u scale = 20 </zoom> <zoom> chr = hs1 start = 160u end = 195u scale = 0.1 </zoom> <zoom> chr = hs2 start = 10u end = 80u scale = 0.1 </zoom> <zoom> chr = hs2 start = 89.5u end = 110u scale = 10 </zoom> <zoom> chr = hs2 start = 87.2u end = 87.8u scale = 40 </zoom> <zoom> chr = hs2 start = 90.5u end = 92u scale = 40 </zoom> <zoom> chr = hs2 start = 93u end = 103u scale = 0.02 </zoom> <zoom> chr = hs2 start = 109.5u end = 112.5u scale = 20 </zoom> <zoom> chr = hs2 start = 115u end = 240u scale = 0.1 </zoom> </zooms> <links> radius = 0.99r crest = 1 color = grey bezier_radius = 0r bezier_radius_purity = 0.5 <link> file = data/5/segdup.txt ribbon = yes thickness = 2 stroke_color = vdgrey stroke_thickness = 2 <rules> flow = continue <rule> condition = var(intrachr) condition = abs(var(pos1) - var(pos2)) < 10Mb show = no </rule> <rule> condition = max(var(size1),var(size2)) < 5000 show = no </rule> <rule> condition = 1 z = eval(int(max(var(size1),var(size2))/5000)) </rule> <rule> condition = var(intrachr) condition = (var(chr1) eq "hs1" && var(start1) < 1Mb) || (var(chr2) eq "hs1" && var(start2) < 1Mb) color = orange stroke_color = dorange </rule> <rule> condition = var(intrachr) condition = (var(chr1) eq "hs1" && var(start1) > 16Mb && var(start1) < 17Mb) || (var(chr2) eq "hs1" && var(start2) > 16Mb && var(start2) < 17Mb) color = lblue stroke_color = dblue </rule> </rules> </link> </links> <plots> <plot> type = heatmap file = data/7/heatmap.zoom-06.txt r1 = 1.16r r0 = 1.12r color = spectral-9-div stroke_thickness = 0 scale_log_base = 0.5 </plot> </plots> <<include etc/housekeeping.conf>> data_out_of_range* = trim
show_bands = no fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 3
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_style> <break_style 2> stroke_color = black stroke_thickness = 2 thickness = 2r </break_style>
<ideogram> <spacing> default = 0.005r break = 0.5r <<include breaks.conf>> </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 = 0.90r thickness = 50p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> label_separation = 10p tick_separation = 3p radius = dims(ideogram,radius_outer) multiplier = 1e-6 label_offset = 0p color = black <tick> spacing = 0.02u size = 5p thickness = 2p show_label = no label_size = 12p format = %.1f </tick> <tick> spacing = 0.1u size = 8p thickness = 2p show_label = yes label_size = 12p format = %.1f </tick> <tick> spacing = 0.5u size = 10p thickness = 2p show_label = yes label_size = 12p format = %.1f </tick> <tick> spacing = 1u size = 12p thickness = 2p show_label = yes label_size = 12p format = %d </tick> <tick> spacing = 5u size = 14p thickness = 2p show_label = yes label_size = 16p format = %d </tick> <tick> spacing = 10u size = 18p thickness = 2p show_label = yes label_size = 20p label_offset = 5p format = %d </tick> </ticks>