[ensembl-dev] how to get genes from unplaced scaffolds via Perl API

Javier Herrero jherrero at ebi.ac.uk
Tue Sep 4 15:11:25 BST 2012


Dear Sergei

You can use

my @slices = @{ $slice_adaptor->fetch_all('toplevel') };

instead. The coordinate system alias "toplevel" corresponds to all the 
so-called top-level sequences, i.e. the chromosomes (if any) and all the 
unplaced scaffolds.

I hope this helps

Javier

On 01/09/12 07:58, Sergei Manakov wrote:
> Hello,
>
> According to GRCm38 description there are 21 chromosomes and 22
> unplaced scaffolds this version of the mouse genome.
>
> How can I get slices for these unplaced scaffolds?
>
> this doesn't work:
>
> my @slices = @{ $slice_adaptor->fetch_all('chromosome') };
>
>
> thanks very much!
> Sergei
>
>
>
>
>

-- 
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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