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

[Andrea Edwards]

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.
>
>
> 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
>>>>
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