[ensembl-dev] Fwd: Re: no chrun exons or genes?

[Paul Flicek]

ChrUn is an artificial construct used by the UCSC genome browser to collect unplaced and unordered contigs on the human assembly in a way that works better for their data model.  In Ensembl these are referred to by their accession number.

Thus there really is no such thing as ChrUn for human.  

For further details about the human assembly please take some time to read about the human assembly at http://www.genomereference.org.


Paul

On 12 May 2011, at 16:02, Andrea Edwards wrote:

> Hi
> 
> Thanks for reply
> 
> Looking further into it, it seems there are no exons or genes on chrun
> for human
> 
> select count(*) from gene g inner join seq_region sr
> using(seq_region_id)where name Regexp 'Un';
> ----------+
> | count(*) |
> +----------+
> |        0 |
> +----------+
> 1 row in set (0.07 sec)
> 
> Why is this?
> 
> 
> 
> On 12/05/11 08:18, Will McLaren wrote:
>> Hi Andrea,
>> 
>> As long as you have variations on the same chromosome together and
>> sorted by position, the order of the chromosomes makes no difference.
>> 
>> Will
>> 
>> On Thursday, 12 May 2011, Andrea Edwards<edwardsa at cs.man.ac.uk>   wrote:
>>> Hi
>>> 
>>> The readme file for VEP recommends input files be sorted by chromosome for whole genome mode. Where do chrUn chromosomes come in the sorting order for this?
>>> 
>>> thanks
>>> 
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>> 
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/