[ensembl-dev] "random" chromosomes form UCSC

[Javier Herrero]

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