[ensembl-dev] "random" chromosomes form UCSC

Javier Herrero jherrero at ebi.ac.uk
Tue Jan 31 17:40:36 GMT 2012


Hi Hiram

That is correct, those contigs are usually in different pieces, although 
some are linked. In particular, AC125149.4 is (the only) part of the 
SuperContig NT_166280. You can access the contig using the Ensembl 
search box, the Location box (in the Location view) and the API (or the 
database).

If you need a SuperContig to contig mapping, it should be faily easy to 
get that information using a Perl script or even a MySQL query.

Javier

On 31/01/12 17:24, Hiram Clawson wrote:
> Good Morning Javier:
>
> Is this one of the cases where I need a ucscToEnsembl mapping table ?
> Are the contigs for these chr*_random sequence in separate pieces
> at Ensembl ?  For example, how would I view AC125149.4 at Ensembl ?
>
> --Hiram
>
> Javier Herrero wrote:
>> Hi Sergei
>>
>> These random chromosomes are not part of the official golden path. 
>> You can translate them into contigs using the 
>> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chr5_random_gold.txt.gz 
>> file. You'll find those contigs in the Ensembl database and you can 
>> create slices for them.
>>
>> I hope this helps
>>
>> Javier
>>
>> On 31/01/12 08:56, Sergei Manakov wrote:
>>> Hello,
>>>
>>> In fasta files per mm9 chromosome in UCSC browser
>>> (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/) there are
>>> "random" chromosome fasta files (e.g. chr5_random.fa.gz), that contain
>>> some interesting sequences.
>>>
>>> Is it possible to retrieve a slice from ensembl for these "random"
>>> chromosomes? Simply putting "5_random"
>>>
>>> $slice_adaptor->fetch_by_region('chromosome', "5_random", $start, 
>>> $end);
>>>
>>> doesn't work...
>>>
>>> thanks!
>>> Sergei
>>>
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>>
>
>

-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK





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