[ensembl-dev] problem loading ncRNA trees

[Javier Herrero]

Hi Julien

Unfortunately, the ncRNA tree pipeline is still fairly recent. At the moment 
we can successfully build most of the trees, but a handful of them are still 
failing.

In this case, both these genes belong to the same family. There are more than 
2000 genes in that one and you can imagine that this might create some 
problems. In this particular case, we were unable to run either RAxML nor 
PRANK on time for the release.

We are looking at ways to improve the pipeline. We already have a few ideas 
and hope to get things sorted, even for such large families.

Javier

On Monday 13 Dec 2010 08:22:14 Julien Roux wrote:
> Dear Ensembl list,
> (I had no answer on my previous mail, so I am reposting this)
> 
> I noticed that quite a lot of the NCTrees fail to load using the API and
> the website (Gene Tree view).
> For example:
> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000222692
> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000215960
> Is there a way to fix/bypass this?
> Thanks a lot
> Julien
> 
> Le 29.11.10 09:26, Julien Roux a écrit :
> > Thank you very much for your answers,
> > 
> > NCTree is indeed working, although some of the methods described in the
> > NCTree Adaptor do not actually work for ncRNAs (for example
> > "fetch_by_Member_root_id")
> > 
> > Another observation is that quite a lot of the NCTrees fail to load
> > using the API. This is also the case using the Gene Tree view of the
> > Ensembl website...
> > For example look at:
> > http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000222692
> > http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000215960
> > 
> > What do you think is happening?
> > Best,
> > Julien
> > 
> > Le 26.11.10 09:41, Albert Vilella a écrit :
> >> Substituting "ProteinTree" for "NCTree" in the adaptor should just work.
> >> 
> >> On Fri, 2010-11-26 at 08:54 +0100, Julien Roux wrote:
> >>> Dear Ensembl team
> >>> 
> >>> Is there a way to access the ncRNA gene trees via the Ensembl perl API?
> >>> (for example miRNA trees like this one:
> >>> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?db=core;g=ENSG000
> >>> 00199024;r=20:3898141-3898218;t=ENST00000362154)
> >>> 
> >>> After some tries, it seems that the usual methods working for protein
> >>> trees do not work for ncRNA trees...
> >>> 
> >>> Thanks for any tip
> >>> Julien
> >> 
> >> _______________________________________________
> >> Dev mailing list
> >> Dev at ensembl.org
> >> http://lists.ensembl.org/mailman/listinfo/dev

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK