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

[Hiram Clawson]

Good Morning Andrea:

The UCSC genome database has a table to translate UCSC chrom names to Ensembl names:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A  -e "select * from ucscToEnsembl;" hg19

In some cases, there is also a coordinate translation offset:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A  -e "select * from ensemblLift;" hg19

--Hiram

Andrea Edwards wrote:
> 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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> 
> 
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