[Genome] Trace Coverage

J.J. Emerson jje at gate.sinica.edu.tw
Wed Aug 1 03:53:28 PDT 2007


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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