[ensembl-dev] Coordinate System anomalies in EnsemblGenomes
Dan Staines
dstaines at ebi.ac.uk
Mon Mar 4 11:43:03 GMT 2013
On 03/04/2013 11:33 AM, PATERSON Trevor wrote:
> I think that my temporary crisis in comprehension is due to a
> particular problem with the bacterial assembly example given, all
> 244 of the sequence regions labelled as top level (with coordsystem
> = 'supercontig') seem to be identical to the 244 sequence regions
> belonging to the sequence_level coord system ('contig') - so it
> appears that in fact no "assembly" has been imported into
> ensemblgenomes for this species.
For the pipeline used for bacteria, we only use set of sequences which
equate to the highest level of assembly we can find (chromosomes or
supercontigs). Following Ensembl convention, we separate features and
sequences onto different coordinate systems which means we get two
identical sets of seq_regions, one of which is toplevel (and hence has
features) and one of which has the sequence attached via the DNA table -
this has always been the case for bacteria and has remained the same.
Dan.
--
Dan Staines, PhD Ensembl Genomes Technical Coordinator
EMBL-EBI Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
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