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 = hs1;hs2;hs3;hs4;hs5;hs6;hs7;hs8 chromosomes_display_default = yes <links> <link> file = data/5/segdup.bundle4.txt radius = 0.95r bezier_radius = 0r color = vvdgrey thickness = 2 record_limit = 2500 <rules> # if a rule is triggered, continue testing with other rules flow = continue # remap the color of the link to the first chromosome <rule> condition = 1 color = eval(sprintf("%s_a4",var(chr1))) </rule> # Alter radial position of one or both ends of a link, depending # on its position. The function on(RX) tests whether a link # is on a chromosome matching the regular expression RX. <rule> # to/from hs1 condition = on(hs1$) radius = 0.85r </rule> <rule> # to hs10, hs11 or hs12 condition = to(hs1) radius2 = 0.75r </rule> <rule> # from hs10, hs11, hs12 condition = from(hs1) radius1 = 0.75r </rule> <rule> # from hs14 and has start beyond 100mb condition = from(hs14) && var(start1) > 100mb radius1 = 1r+50p z = 5 thickness = 3 color = blue </rule> <rule> # to hs5 and has end within 50mb of position 100mb condition = to(hs5) && abs(var(start2) - 100mb) < 50mb radius2 = 1r+50p z = 5 thickness = 3 color = red </rule> </rules> </link> </links> <<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 = 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>