[ensembl-dev] Fwd: Re: no chrun exons or genes?
edwardsa at cs.man.ac.uk
Thu May 12 17:11:53 BST 2011
thank-you kindly for clarifying that. Is there a flag/field in the
ensembl schema which identifies chrun sequences? Even better is there a
utility offered by ensembl to map ucsc chrun data to ensembl data?
On 12/05/11 16:33, Paul Flicek wrote:
> 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.
> On 12 May 2011, at 16:02, Andrea Edwards wrote:
>> 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.
>>> On Thursday, 12 May 2011, Andrea Edwards<edwardsa at cs.man.ac.uk> wrote:
>>>> 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?
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