UNPKG

ibowankenobi-i-pv

Version:

Interactive Protein Sequence VIsualization/Viewer - Interactive Circos

65 lines (44 loc) • 2.08 kB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
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>