[ensembl-dev] RNAseq gene models

[Thibaut Hourlier]

Dear Genomeo,
We do not use the ENSG prefix to RNASeq genes because they were not generated using the Ensembl pipeline.

You can use the API to access the rnaseq database, homo_sapiens_rnaseq_75_37, on the public server: http://www.ensembl.org/info/data/mysql.html or you can have a local version: ftp://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_rnaseq_75_37/. You will also need the core database in this case.

Regards
Thibaut

On 30 Apr 2014, at 14:00, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
> 
> rnaseq gene models such as RNASEQG00000132922:
> 
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=rnaseq;g=RNASEQG00000054976;r=7:86273230-86494200;t=RNASEQT00000054976
> 
> don't have the ENSG name format. Is there a reason for not incorporating these into the Ensembl gene set? These may not be novel genes and might be alternative splice transcripts for genes which already exist in the Ensembl gene set.
> 
> While the body map bam files can be downloaded from this location:
> 
> ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/rnaseq
> 
> is it also possible to download the rnaseq gene models displayed on the track (not the bam files)?
> 
> Thanks.
> 
> -- 
> G.
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