[Genome] GC Percent selected fields

[Brooke Rhead]

Hello Peter,

I am not sure how you were able to get "selected fields" as an output 
option for the gc5base table.  The gc5Base table, like all wiggle-type 
tables, simply contains pointers to data files.  The data files contain 
the actual information.  (We do this because the tables would otherwise 
be extremely large.)  The "data points" output option fetches the actual 
data in the region specified from the data files, and presents it in 
variableStep format.

You can read about the wiggle data format here:

http://genome.ucsc.edu/goldenPath/help/wiggle.html

The information in the gc5Base table is not very interesting to most 
users (just confusing), so the "all fields" and "selected fields" output 
options are not made available.  However, if you are actually looking 
for the contents of the table, you can find it on our downloads server, 
here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/

(the file is called gc5Base.txt.gz).

If you are looking for the actual data underlying the GC Percent track, 
you can use the "data points" option in the Table Browser.  This can 
fetch up to 10 million rows of information at one time.  If you are 
trying to download this information for an entire genome, this will take 
multiple Table Browser queries (about 60 for the hg18 assembly).  If 
this is indeed what you are looking for, let us know, and we can make 
the data file available for download.

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

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Peter Brooks wrote:
> Hello
> 
> In Table Browser, I tried to download a table of GC percent with a 
> limited choice of fields.
> In "output format", only the 3 choices: data points, bed format or 
> custom track were available.
> Output format did not include the usual prompt "selected fields form 
> primary and related tables".
> (So the only possible output was the listing of GC% for sequential 5 bp 
> segments.)
> 
> I tried another type of table and found the "selected fields form 
> primary and related tables" as usual in Output format.
> 
> Then when I went Back in Firefox, and reselected gc5Base, I was able to 
> select fields and download.
> So I got the data but I would appreciate any suggestions about how to 
> use Table Browser to avoid this problem.
> 
> Thank you
> 
> Peter Brooks
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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