Generating karyotype files from UCSC assembly tables
----------------------------------------------------

The parse.assembly script parses an Assembly table to create a
karyotype file for Circos. The script will not work on a Chromosome
Band file (use ../parse.karyotype for this).

  parse.assembly bostau7.txt bt > karyotype.cow.txt

The prefix, e.g. bt, will be used to label the chromosomes (e.g. bt1,
bt2 ... ) By default, "chr" is used. It is customary for Circos to use
the species acronym for chromosome prefixes, instead of the generic
'chr'. Using a different prefix for each species avoids chromosome
name collisions (e.g. human and mouse chromosomes 1 are distinguished
as hs1 and mm1).

To download data tables, see http://genome.ucsc.edu/cgi-bin/hgTables


Unanchored segments
-------------------

It's likely that your assembly will contain many unanchored
chromosomes (chrUn_*). You probably want to remove these from the
karytoype file. To do this, use grep -v to remove lines with PREFIX+un in them

  parse.assembly bostau7.txt bt | grep -v btun > karyotype.cow.txt


Chromosome colors
-------------------

The last field in each line of the karyotype file is the chromosome
color. If you set 'fill' in the <ideogram> block, this is the color
that will be used to tint the ideogram in the figure.

The default human chromosome color scheme defines colors

  chr1 ... chr22, chrx, chry, chrm, chrun

and is used by the UCSC genome browser. These colors are defined in

  etc/colors.ucsc.conf

along with colors for cytogenetic bands, named after the stain
properties (e.g. gpos100, gpos75, gneg, gvar, acen, stalk, etc).

Depending on the name and number of your chromosome, your karyotype
file could include colors that are not defined (e.g. chr29). It is up
to you to define these.

You can add new colors to circos by including another <colors> block
with your color definitions

  # default color definitions
  <<include etc/colors_fonts_patterns.conf>>

  # add more colors
  <colors>
  ...
  chr28 = 110,110,110
  chr29 = 100,100,100
  ...
  </colors>
