[Genome] L

[Hiram Clawson]

Good Morning Deepa:

Please note the discussion of using hgWiggle with the database
table dumps at:
	http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database

You want to use the database table dump from:
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/wgEncodeUcsdNgTaf1Signal.txt.gz
And the corresponding .wib file at:
ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/encode/wib/wgEncodeUcsdNgTaf1Signal.wib

The file you were working with was the original ascii data which
has been encoded to become the gEncodeUcsdNgTaf1Signal.txt SQL table
and wgEncodeUcsdNgTaf1Signal.wib file.

You can also extract these numbers with the table browser.
Enter your genomic coordinates as a custom track, or a set
of defined regions, and intersect with this LI TAF1 Signal track.

--Hiram

Pai, Deepa wrote:
> Hi,
>      Given a set of genomic coordinates, I want to calculate the
> conservation score for the region.
> 
>       Similar question has been asked before, but I havent been
> successful using the hgWiggle.
> 
>  
> 
>        For hg18,
> 
>        I have downloaded and unzipped wgEncodeUcsdNgTaf1Signal.wigVar.
> 
>        Also, downloaded phastCons17way.wib to the same folder.
> 
>         $ ln -s wgEncodeUcsdNgTaf1Signal.wigVar
> wgEncodeUcsdNgTaf1Signal.wig
> 
>  
> 
>         Now,  when I run hgWiggle, on the flat files, I get the error
> message,
> 
>          [paid at moria wig]$ ~/bin/i386/hgWiggle
> -position=chr6:26195715-26195740 wgEncodeUcsdNgTaf1Signal.wig
> 
>         #       no values found with these constraints
> 
>         [paid at moria wig]$ ~/bin/i386/hgWiggle -chr=chr12
> wgEncodeUcsdNgTaf1Signal.wig
> 
>         #       no values found with these constraints
> 
>  
> 
>         Is it because the .wib and .wig file names are different? How
> can I link them?
> 
>  
> 
> Thanks
> 
> Deepa.