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

[Will Chow]

I'm not sure if theres a seq_region_attrib that tags these scaffolds.

They are in the database though.

Via ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38/Primary_Assembly/

There's a list of the unplaced scaffolds and their accessions, and while I only looked at one, they seem to be in the core database.  So worse case scenario is you may have to fetch slice per name.  But I may be wrong.

Best ask someone from the ensembl/ensembl gene build team? who created the ensembl build.

Will

MSCHRUN_CTG1	GL456239.1
MSCHRUN_CTG2	GL456367.1
MSCHRUN_CTG3	GL456378.1
MSCHRUN_CTG4	GL456381.1
MSCHRUN_CTG5	GL456382.1
MSCHRUN_CTG6	GL456383.1
MSCHRUN_CTG7	GL456385.1
MSCHRUN_CTG9	GL456390.1
MSCHRUN_CTG10	GL456392.1
MSCHRUN_CTG11	GL456393.1
MSCHRUN_CTG12	GL456394.1
MSCHRUN_CTG13	GL456359.1
MSCHRUN_CTG14	GL456360.1
MSCHRUN_CTG15	GL456396.1
MSCHRUN_CTG16	GL456372.1
MSCHRUN_CTG17	GL456387.1
MSCHRUN_CTG18	GL456389.1
MSCHRUN_CTG19	GL456370.1
MSCHRUN_CTG20	GL456379.1
MSCHRUN_CTG21	GL456366.1
MSCHRUN_CTG22	GL456368.1
MSCHRUN_CTG23	JH584304.1



On 1 Sep 2012, at 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
> 
> 
> 
> 
> 
> -- 
> EMBL-EBI and Wellcome Trust Sanger Institute
> 
> tel: 00441223492675
> 
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