[ensembl-dev] how to get genes from unplaced scaffolds via Perl API
Will Chow
wc2 at sanger.ac.uk
Tue Sep 4 15:27:53 BST 2012
Javier is right, you can use top-level. I thought it might return more than the advertised 22 unplaced, but I might be just looking at the wrong query.
mysql> select coord_system.name, coord_system_id, count(*) from seq_region inner join seq_region_attrib using (seq_region_id) inner join coord_system using (coord_system_id) where attrib_type_id = 6 group by coord_system_id;
+------------+-----------------+----------+
| name | coord_system_id | count(*) |
+------------+-----------------+----------+
| scaffold | 2 | 44 |
| chromosome | 3 | 22 |
+------------+-----------------+----------+
2 rows in set (0.00 sec)
All the best,
Will
On 4 Sep 2012, at 15:11, Javier Herrero wrote:
> 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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