[Genome] Trace Coverage

[Brooke Rhead]

Hi J.J.,

Thank you for the compliments on the Browser!

We do not display all of the information you are seeking, although the 
clone coverage track may be interesting to you and at least lead part 
way to what you need.

Also, we do have links to the NCBI human genome assembly documentation 
from our hg18 gateway page, here:

http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg18

Scroll down to "assembly details" section and look for the "NCBI Build 
36.1 Statistics" link and the "NCBI Build 36.1 release notes" link.

We do not display the Celera WGS assembly of the human genome.

I hope this information is useful.  If you have further questions, 
please do not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



J.J. Emerson wrote:
> Hello,
> 
> I am using your genome browser, which is beautiful, by the way.   
> Anyway, I have a few questions for you with regard to the tracks  
> present for the public human genome project's trace coverage.
> 
> The first question that I have, is how much information on coverage  
> do you have?  A bit more specifically, do you have coverage  
> information with regards to which sequencing method that coverage was  
> collected from?
> 
> The questions I'm looking for don't seem to be directly addressed in  
> the browser or descriptions of the tables underlying the brower's  
> coverage track:
> 
> http://genome.cse.ucsc.edu/cgi-bin/hgTables? 
> db=hg18&hgta_group=map&hgta_track=clonePos&hgta_table=clonePos&hgta_doSc 
> hema=describe+table+schema
> 
> I'm specifically looking for a way to determine the fold coverage of  
> within clone shotgun sequence (not finishing sequence) on as fine a  
> scale as possible.  Ideally, I would have a sequence of integers  
> representing the fold coverage along a chromosome.  But I can imagine  
> the data coming in many other forms, such as in a series of mappings  
> between trace sequences and the assembled reference sequence.
> 
> Finally, do you have anything similar for the Celera project's WGS  
> assembly/traces?
> 
> Thanks a lot!  Again, the job you do with the data is amazing.  My  
> hat's off to you yet again.
> 
> Cheers,
> 
> J.J.
> _______________________________________________
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