<<include /software/circos/0.69-9/circos-0.69-9/etc/colors_fonts_patterns.conf>>

<<include /software/circos/0.69-9/circos-0.69-9/etc/housekeeping.conf>>

<<include /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2023-09-26-Novogene-NovaSeq/ideogram.conf>>
<<include /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2023-09-26-Novogene-NovaSeq/ticks.conf>>

<image>
<<include /software/circos/0.69-9/circos-0.69-9/etc/image.conf>>
</image>

karyotype = /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2023-09-26-Novogene-NovaSeq/chr.karyotype

chromosomes_units           = 1000
chromosomes_display_default = yes
chromosomes                 = chr

<plots>

# <plot>
# type = tile
# file = /oak/stanford/groups/akundaje/marinovg/papers/2020_organelles_TFs/2018-07-14-ENCODE-TFs/config-files/hg19.chrM.minus.protein_coding.tile
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = dorange
# color = dorange
# r0 = 0.98r
# r1 = 0.99r
# </plot>

type      = histogram
thickness = 0.5



<plot>
type        = histogram
file        = scaffolds_reoriented.GCskew.500bp.chr.cumulative
r0          = 0.50r
r1          = 0.75r
min         = 0
max         = 300
extend_bin  = no
fill_under = yes
fill_color  = red
color       = red
thickness   = 0.1
orientation = out
</plot>

<plot>
type        = histogram
file        = scaffolds_reoriented.GCskew.500bp.chr.bins
r0          = 0.30r
r1          = 0.50r
min         = -0.5
max         = 0.5
extend_bin  = no
fill_under = yes
fill_color  = lblue
color       = lblue
thickness   = 0.1
orientation = out
</plot>

<plot>
type        = histogram
file        = scaffolds_reoriented.GCskew.500bp.chr.zeros
r0          = 0.399r
r1          = 0.401r
min         = -0.01
max         = 0.01
extend_bin  = no
fill_under = yes
fill_color  = black
color       = black
thickness   = 0.1
orientation = out
</plot>

<plot>
type        = histogram
file        = scaffolds_reoriented.GCskew.500bp.chr.zeros
r0          = 0.499r
r1          = 0.501r
min         = -0.01
max         = 0.01
extend_bin  = no
fill_under = yes
fill_color  = black
color       = black
thickness   = 0.1
orientation = out
</plot>

<plot>
type      = tile
file      = chr.protein.tile.plus
r0        = 0.82r
r1        = 0.87r
layers    = 5
margin    = 0.2u
thickness = 12
padding   = 6
layers_overflow  = hide
orientation      = out
stroke_thickness = 1
stroke_color     = grey
color            = red
# <rules>
# <rule>
# condition = var(size) < 5kb
# color     = lgrey
# </rule>
# </rules>
</plot>

<plot>
type      = tile
file      = chr.protein.tile.minus
r0        = 0.87r
r1        = 0.92r
layers    = 5
margin    = 0.2u
thickness = 12
padding   = 6
layers_overflow  = hide
orientation      = out
stroke_thickness = 1
stroke_color     = grey
color            = blue
# <rules>
# <rule>
# condition = var(size) < 5kb
# color     = lgrey
# </rule>
# </rules>
</plot>


<plot>
type      = tile
file      = chr.rRNA.tile
r0        = 0.96r
r1        = 0.98r
layers    = 5
margin    = 0.2u
thickness = 12
padding   = 6
layers_overflow  = hide
orientation      = out
stroke_thickness = 1
stroke_color     = grey
color            = orange
</plot>

<plot>
type      = tile
file      = chr.tRNA.tile
r0        = 0.92r
r1        = 0.96r
layers    = 5
margin    = 0.2u
thickness = 12
padding   = 6
layers_overflow  = hide
orientation      = out
stroke_thickness = 1
stroke_color     = grey
color            = black
</plot>


</plots>


