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