This is a file used in the Circos software. Can someone help me understand what it means?
0
0
Entering edit mode
5.9 years ago

This is a snippet of code that is used as a base case for running the software Circos on. This is the link to said file: https://github.com/vigsterkr/circos/blob/master/data/karyotype.human.txt. Can anyone explain to me the differences between chromosomes and bands and what the file type is reading? Even a link to Circos documentation is fine. If I can just understand what the software needs, I can feed the data I need to visualize to the software.

# Human chromsome sizes and cytogenetic band position.
# Data based on hg18 assembly.
chr - hs1 1 0 247249719 green
chr - hs2 2 0 242951149 green
chr - hs3 3 0 199501827 green
chr - hs4 4 0 191273063 green
chr - hs5 5 0 180857866 green
chr - hs6 6 0 170899992 green
chr - hs7 7 0 158821424 green
chr - hs8 8 0 146274826 green
chr - hs9 9 0 140273252 green
chr - hs10 10 0 135374737 green
chr - hs11 11 0 134452384 green
chr - hs12 12 0 132349534 green
chr - hs13 13 0 114142980 green
chr - hs14 14 0 106368585 green
chr - hs15 15 0 100338915 green
chr - hs16 16 0 88827254 green
chr - hs17 17 0 78774742 green
chr - hs18 18 0 76117153 green
chr - hs19 19 0 63811651 green
chr - hs20 20 0 62435964 green
chr - hs21 21 0 46944323 green
chr - hs22 22 0 49691432 green
chr - hsX X 0 154913754 green
chr - hsY Y 0 57772954 green
band hs1 p36.33 p36.33 0 2300000 gneg
band hs1 p36.32 p36.32 2300000 5300000 gpos25
band hs1 p36.31 p36.31 5300000 7100000 gneg
band hs1 p36.23 p36.23 7100000 9200000 gpos25
band hs1 p36.22 p36.22 9200000 12600000 gneg
band hs1 p36.21 p36.21 12600000 16100000 gpos50
band hs1 p36.13 p36.13 16100000 20300000 gneg
band hs1 p36.12 p36.12 20300000 23800000 gpos25
band hs1 p36.11 p36.11 23800000 27800000 gneg
band hs1 p35.3 p35.3 27800000 30000000 gpos25
band hs1 p35.2 p35.2 30000000 32200000 gneg
band hs1 p35.1 p35.1 32200000 34400000 gpos25
band hs1 p34.3 p34.3 34400000 39600000 gneg
band hs1 p34.2 p34.2 39600000 43900000 gpos25
band hs1 p34.1 p34.1 43900000 46500000 gneg
band hs1 p33 p33 46500000 51300000 gpos75
band hs1 p32.3 p32.3 51300000 56200000 gneg
band hs1 p32.2 p32.2 56200000 58700000 gpos50
band hs1 p32.1 p32.1 58700000 60900000 gneg
band hs1 p31.3 p31.3 60900000 68700000 gpos50
band hs1 p31.2 p31.2 68700000 69500000 gneg
band hs1 p31.1 p31.1 69500000 84700000 gpos100
band hs1 p22.3 p22.3 84700000 88100000 gneg
band hs1 p22.2 p22.2 88100000 92000000 gpos75
band hs1 p22.1 p22.1 92000000 94500000 gneg
band hs1 p21.3 p21.3 94500000 99400000 gpos75
band hs1 p21.2 p21.2 99400000 102000000 gneg
band hs1 p21.1 p21.1 102000000 107000000 gpos100
band hs1 p13.3 p13.3 107000000 111600000 gneg
band hs1 p13.2 p13.2 111600000 115900000 gpos50
band hs1 p13.1 p13.1 115900000 117600000 gneg
band hs1 p12 p12 117600000 120700000 gpos50
band hs1 p11.2 p11.2 120700000 121100000 gneg
band hs1 p11.1 p11.1 121100000 124300000 acen
band hs1 q11 q11 124300000 128000000 acen
band hs1 q12 q12 128000000 142400000 gvar
band hs1 q21.1 q21.1 142400000 148000000 gneg
band hs1 q21.2 q21.2 148000000 149600000 gpos50
band hs1 q21.3 q21.3 149600000 153300000 gneg
band hs1 q22 q22 153300000 154800000 gpos50
band hs1 q23.1 q23.1 154800000 157300000 gneg
band hs1 q23.2 q23.2 157300000 158800000 gpos50
band hs1 q23.3 q23.3 158800000 163800000 gneg
band hs1 q24.1 q24.1 163800000 165500000 gpos50
band hs1 q24.2 q24.2 165500000 169100000 gneg
circos file type software sequencing • 1.3k views
ADD COMMENT
1
Entering edit mode

Link to the documentation on karyotypes:

http://circos.ca/documentation/tutorials/ideograms/karyotypes/

ADD REPLY
1
Entering edit mode

Can anyone explain to me the differences between chromosomes and bands and what the file type is reading?

Simple explanation of chromosomes and cytobands (if that is what you are looking for).

ADD REPLY

Login before adding your answer.

Traffic: 2996 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6