[ensembl-dev] "random" chromosomes form UCSC

Hiram Clawson hiram at soe.ucsc.edu
Tue Jan 31 17:24:54 GMT 2012


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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> 





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