[ensembl-dev] Missing latest RefSeq Transcript in MySQL of Ensembl 100 GRCh37

[Helen Schuilenburg]

Hi

The database and VEP caches are in sync. NM_004448.3 is in the database 
and VEP caches.

Running VEP for a variant  using the database without a cache 
NM_004448.3 is returned e.g.

./vep --database --assembly GRCh37 --port 3337 --input_data 
rs1456994901  --refseq

The schema has not changed and NM_004448.3 can be queried using the 
transcript and the xref table 
https://www.ensembl.org/info/docs/api/core/core_schema.html#xref

SELECT stable_id
FROM transcript
WHERE stable_id like '%NM_004448%'

It is best to query using the API instead of querying the database directly.

See core API: https://www.ensembl.org/info/docs/api/core/index.html)

The core tutorial 
https://www.ensembl.org/info/docs/api/core/core_tutorial.html#xrefs

FAQ: How do I access RefSeq annotation in Ensembl? 
grch37.ensembl.org/Help/Faq

Regards

Helen

On 08/06/2020 07:54, Wallace Ko wrote:
> Hi,
>
> I have some variants on the gene ERBB2 annotated by VEP 100 (GRCh37) 
> transcripts NM_004448.3, which seems to be a record from the new 
> RefSeq release.
> However, when I tried to query the transcript table in the MySQL 
> (ensembldb.ensembl.org:3337/homo_sapiens_otherfeatures_100_37 
> <http://ensembldb.ensembl.org:3337/homo_sapiens_otherfeatures_100_37>) 
> , there's no result for this stable_id.
>
> When querying all transcripts of the accession without version (select 
> * from transcript where stable_id like 'NM_004448%'), there are only 
> results for NM_004448.2.
>
> Are the database and cache not in sync yet? Or is the database schema 
> changed so that I'll need to query in another way?
>
> Regards,
> Wallace Ko
>
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