[Bioperl-l] UCSC database -> GFF

[Lincoln Stein]

Hi Allen,

I hope someone (Mummi?) will pick it up.  It's necessary now that NCBI has 
decided to make their human annotations effectively unloadable.  Maybe 
ENSEMBL can have a look at their EMBL output and try to find a way to get 
more track info into it?

Lincoln


On Tuesday 17 June 2003 04:23 pm, Allen Day wrote:
> I wrote it ~1 year ago.
>
> -Allen
>
> On Tue, 17 Jun 2003, Lincoln Stein wrote:
> > Where did that come from?  I was just talking with Mummi about how badly
> > we need this and how difficult it will be to do it right.
> >
> > Lincoln
> >
> > On Tuesday 17 June 2003 02:07 pm, Jason Stajich wrote:
> > > Does core/scripts/Bio-DB-GFF/load_ucsc.pl work for you?
> > >
> > > On Tue, 17 Jun 2003, Paul Edlefsen wrote:
> > > > The Generic Genome Browser comes with many helpful scripts for
> > > > converting various data sources into GFF format.  I am wondering if
> > > > anyone in the bioperl community has written one for the UCSC data, as
> > > > is available at
> > > > ftp://genome.cse.ucsc.edu/goldenPath/10april2003/database and
> > > > described at http://genome.ucsc.edu/goldenPath/gbdDescriptions.html
> > > > -- I noticed that  Allen Day wrote some handy aggregators for that
> > > > data such as Bio::DB::GFF::ucsc_genscan, so I wanted to check before
> > > > I start writing Generic-Genome-Browser/bin/process_ucsc.PLS.
> > > >
> > > > Thanks,
> > > >
> > > >   :Paul

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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