[ensembl-dev] Transcripts missing in Mus_musculus.GRCm38.102.gtf.gz and Mus_musculus.GRCm38.102.gff3.gz

[Thomas Danhorn]

As far as I know, these GTFs/GFFs only contain genes and transcripts from 
the primary assembly, i.e. not from patches.  I suspect 
http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gtf.gz
might contain such transcripts.

Best wishes,

Thomas


On Tue, 26 Oct 2021, Hervé Pagès wrote:

> Hi,
>
> Does anybody know why transcript ENSMUST00000230762 is missing from the 
> GTF and GFF3 files for Mus musculus in Ensembl release 102?
>
> ENSMUST00000230762 is a transcript present in the 
> mus_musculus_core_102_38 db. It's located on novel-patch sequence 
> CHR_WSB_EIJ_MMCHR11_CTG3 from GRCm38.p6. But for some reason it's not in 
> the Mus_musculus.GRCm38.102.gtf.gz or Mus_musculus.GRCm38.102.gff3.gz 
> files found here 
> http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/ and here 
> http://ftp.ensembl.org/pub/release-102/gff3/mus_musculus/
>
> Furthermore, it seems that the GTF and GTF3 files are missing 2079 
> transcripts compared to the mus_musculus_core_102_38 db. Anybody knows 
> what's going on?
>
> Thanks,
> H.
>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github at gmail.com
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: 
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
>