circos-session 1 Lesson 10 Drawing Multiple Genomes

karyotypes of actual genomes can be drawn from data available through the UCSC genome browser table viewer.

karyotype information about a genome can be obtained by selecting --group-- Mapping and Sequencing Tracks and --track-- Chromosome Band or Chromosome Band(Ideogram).

 

show all the human chromosomes

karyotype = ../../data/karyotype/karyotype.human.txt

./etc/circos.conf
#karyotype =  data/karyotype/karyotype.human.txt
#karyotype = data/karyotype/karyotype.mouse.txt
karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt

chromosomes_units           = 1000000
chromosomes_display_default = yes

<<include ideogram.conf>>

<<include ticks.conf>>

<<include ../../etc/image.conf>>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
~                                                                                                                                                             
~                                                                                                                                                             
~                                                   

 

#./etc/ideogram.conf
<ideogram>

<spacing>
default = 10u
#default = 0.01r
</spacing>

<<include ../../etc/ideogram.conf>>

label_size*            = 12
label_radius*          = dims(ideogram,radius) + 0.135r
band_stroke_thickness* = 0
band_transparency*     = 4

#thickness*        = 10p
#stroke_thickness* = 0

#label_format = eval(sprintf("%s",var(chr)))

</ideogram>

~               

 

#./etc/ticks.conf
show_ticks          = yes
show_tick_labels    = yes

<ticks>
label_font      = default
radius          = dims(ideogram,radius_outer)
label_offset    = 5p
multiplier      = 1e-6
color           = black
label_size      = 10p
show_label      = yes
format          = %d

<tick>
spacing     = 20u
#spacing     = 50u
size        = 8p
thickness   = 2p
#thickness   = 1p
</tick>

</ticks>
~                                                                                                                                                             
~                                                                                                                                                             
~                                                                                                                                                             
~                   

FIgure 2

show mouse genome

figure 29

Chromosome Color Scheme

Color convention to index human chromosomes, are defined in the color definition file etc/color.ucsc.conf  in the Circos distribution.  ChrM is the mitochondrial chromosome and chromosome Un  is a concatenation of all unanchored sequence (Sequene that has not yet been , or cannot be , associated with a specific chromosome)

#./circos-0.65-6/etc/colors.uscs.conf
# Also define colors for 'hs' human chr prefix
hs1  = chr1
hs2  = chr2
hs3  = chr3
hs4  = chr4
hs5  = chr5
hs6  = chr6
hs7  = chr7
hs8  = chr8
hs9  = chr9
hs10 = chr10
hs11 = chr11
hs12 = chr12
hs13 = chr13
hs14 = chr14
hs15 = chr15
hs16 = chr16
hs17 = chr17
hs18 = chr18
hs19 = chr19
hs20 = chr20
hs21 = chr21
hs22 = chr22
hs23 = chr23
hsX  = chrX
hs24 = chr24
hsY  = chrY
hsM  = chrM
hs0  = chr0
hsUn = chrUn
hsNA = chrNA

show all the chromosomes of human and mouse

Figure  32