Question: Detecting non-exonic conserved regions
0
gravatar for IP
2.5 years ago by
IP550
Denmark/University of Copenagen
IP550 wrote:

Hi!

I am trying to detect conservation in non exonic regions of the human genome. What I have is is a bed file obtained from the UCSC genome browser Cons Indels MmCf Track. This track shows conserved regions in the genome. When I displayed the file in the genome browser, I can see that there are regions showing a lot of tracks within specific regions that are non exonic. What I would like to do is to convert this bed file with the tracks to a x,y signal and then run a signal detection algorithm on it to detect those conserved regions.

I have an idea about the signal detection algorithm I am going to run, but I am not sure about how to go from a bed file to a x,y signal. Does anyone have an idea?

Thanks a lot for it,

By the way, if you think that I am not aproaching my problem in a proper way, let me know :)

EDIT:

My bed file is a BED3 file

signal detection bed • 695 views
ADD COMMENTlink modified 2.5 years ago by Chirag Nepal2.2k • written 2.5 years ago by IP550
1
gravatar for Chirag Nepal
2.5 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

You can download CNE (conserved noncoding elements) from ANCORA browser http://ancora.genereg.net/ These conserved elements are outside exons. You can download regions based on different threshold (70%conservation, 80%, 90% and so on) and also based on conserved with respect (mouse, frog or zebrafish). Download data from ANCORA and intersect with regions of your interest.

ADD COMMENTlink written 2.5 years ago by Chirag Nepal2.2k
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