Problem making Virus Karyotype

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Ibk

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Feb 24, 2025, 5:00:10 PMFeb 24
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Hi,

I am trying to make a single patterned Karyotype for my virus genome that is 185kb. I want minor ticks plotted every 1kb and major ticks every 50kb. I want alternate black and white color in the karyotype every 10kb. I wrote this conf file but its not giving me the color pattern.

# circos.conf
# make circos plot of virus genome with gene tracks

# Define the karyotype file
karyotype = Virus_karyotype.txt

# Define the chromosomes to display
chromosomes_units = 1000
chromosomes_display_default = yes

<ideogram>
<spacing>
default = 0.005r
</spacing>

radius    = 0.80r
thickness = 15p
fill      = yes
stroke_color = dgrey
stroke_thickness = 2p

# Enable cytobands
show_bands = yes
band_stroke_thickness = 1p
band_transparency = 1

band_colors = grey, blue, gren, red # Alternating colors
</ideogram>

# Define the ticks
 
show_ticks          = yes
show_tick_labels    = yes

<ticks>
skip_first_label     = no
skip_last_label      = no
radius               = dims(ideogram,radius_outer)
tick_separation      = 2p
min_label_distance_to_edge = 0p
label_separation = 5p
label_offset     = 5p
label_size       = 16p
multiplier       = 1e-3  # Converts bp to kb
color            = black

<tick>
size           = 10p
thickness      = 2p
spacing        = 1000   # Every 1kb
show_label     = yes
label_size     = 20p
label_offset   = 5p
format         = %d kb
</tick>

<tick>
size           = 15p
thickness      = 4p
spacing        = 50000   # Every 50kb
show_label     = yes
label_size     = 24p
label_offset   = 10p
format         = %d kb
</tick>
</ticks>

#################
My virus_karyotype.txt is
# Chromosome definition
chr - virus virus 0 185823 grey

Thanks for your help
Ibk
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