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

[Hervé Pagès]

That's it. These *.chr_patch_hapl_scaff.* files seem indeed to contain 
the full db dump. Thanks!

Cheers,
H.


On 26/10/2021 16:22, Thomas Danhorn wrote:
> 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
>>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github at gmail.com