OmicCircos mapping data file.
2
0
Entering edit mode
abdul rawoof ▴ 60
@abdul-rawoof-5869
Last seen 2.7 years ago
United States

Hi all,
 

Could anyone can help me to create mapping data file format used in OmicCircos.
I want to make "mapping data file" for my expression data. I have a set of genes for which I got chromosome start and chromosome end position.
As mentioned in OmicCircos the mapping data file have chromosome position ( "Po") , I tried to get it for my set of genes but couldn't get it.

From where I can get this information.

Thanks

omiccircos • 1.0k views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 18 hours ago
United States

Looking at the vignette for OmicCircos, there is an example mapping file on page 4, and the vignette states that the second column ('Po' column) is the position. It's not clear what 'position' means in this context, so let's do an experiment!

The first gene is ISG15. I don't see the build, but it is TCGA data, so I assume it is a bit old, probably hg18. So I went to UCSC's browser, punched in that gene name and got:

ISG15 (uc001acj.2) at chr1:938710-939782

as the first hit for the hg18 build. But the value in the vignette is 939245.5, which is somewhere between the start and end of that gene. So I used my trusty slide rule to calculate the mean of the start/end value that I get from UCSC, and I get 939246, which is close enough for government work. So I assume that the position is the middle of the gene, which you can easily compute if you have the start/end values.

 

ADD COMMENT
0
Entering edit mode

Thanks, It's really helpful for me...I also thought in the same way but I was using hg19 built thats why I was not getting correct position value.

ADD REPLY
0
Entering edit mode
@hu-ying-nihnci-e-6375
Last seen 5.5 years ago
United States

OmicCircos was updated http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html

Please let me know if you have any questions.

Thanks

Ying 

yhu@mail.nih.gov

ADD COMMENT

Login before adding your answer.

Traffic: 219 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