[DAS] LDAS vs Dazzle

Ewan Birney birney@ebi.ac.uk
Sat, 5 Jan 2002 09:54:43 +0000 (GMT)

On Fri, 4 Jan 2002, jfreeman wrote:

> Hello all,
> Thanks for the quick response!
> Ewan Birney wrote:
> > 
> > Just to make sure people don't think something weird is going on:
> > 
> > (a) Ensembl's "assembly" is (currently) a particular UCSC golden path and
> > soon will be one of the NCBI golden paths. Ensembl doesn't make assemblies
> > - we just choose one to use.
> I never meant to imply that Ensembl's choice of any of the golden paths
> in the past or present or future was or is or will be suspect, from my
> last note.  I was, badly, making the point that if you decide to map
> your data onto any one of them the cost of doing so leads you to want to
> pick one, as Ensembl does, rather than map to them all.  That is the
> source for a natural lock-in for anyone doing the mapping, if you would
> like enjoy the utility of the Ensembl package then you go with what
> Ensembl chose when you do your mapping.  The choice of a particular
> golden path is Ensembl's prerogative as you mention, but the rationale
> for the change is not clearly understood, given your cost of remapping
> your data, and my cost of doing the same.  If you have the time to
> educate me, I would like to understand what leads to the Ensembl group
> choose a particular golden path, and this will help me explain the value
> of the system, given the remapping costs, internally, and might be of
> some use to others on this list.


I think this is the sort of conversation one needs to have over beers. 

  - We have to move golden paths because we want to encorporate new data
(remember - the human genome is being finished all the time).

  - currently there are two golden paths per freeze date of the data (NCBI
and UCSC) but they are both converging to the same set of underlying data
inside the sequencing centres for each chromosome. From here on in for
human assemblies it is really a rather boring data tracking exercise (but
of course very necessary).

  - We've spent the last 9 months setting up this data tracking system in
a better way (for the people in the know these are the "TPF files"). To
help everyone work together we are now focusing on just one assembly
series - NCBI - with the agreement of UCSC (UCSC is going to keep NCBI
honest and move onto bigger/better things).

   Does this make sense?