[ensembl-dev] mod(mdg4)-FBgn0002781 does not exist in GTF gene setfor Drosophila melanogaster

[Rodriguez.Jose_Manuel]

Yes, it's a "weird" case.

Thanks for your answer. I hope one day you resolve the problem.

Best Regards,
J

> On 21/08/2015, at 14:47, "Amonida Zadissa" <amonida at ebi.ac.uk> wrote:
> 
>> On 21/08/2015 12:23, José Manuel Rodríguez wrote:
>> Hi Amonida,
>> 
>> How are you?
> 
> I'm fine thanks, hope you're well too.
> 
>>> 
>>> The FBgn0002781 gene contains a trans-splicing transcript and
>>> unfortunately our GTF dumping pipeline can't handle cases where the
>>> gene and transcript are on different strands.
>> 
>> Sad news… Do you think to include these cases in your GTF dumping?
>> Maybe for the next release or the e83 release?
> 
> Actually, this is the only trans-splicing gene in the entire set of
> Ensembl annotations. So the current frequency of their present is very
> low. Regardless though we are looking into if/how to represent such
> genes in Ensembl; at the moment this gene just breaks the pipeline. I
> can't tell you when it will be resolved though.
> 
> Best regards,
> Amonida
> 
>> Cheers,
>> J
>> 
>>> 
>>> Best regards,
>>> Amonida
>>> 
>>> José Manuel Rodríguez <jmrodriguez at cnio.es> wrote:
>>> 
>>> Hi all,
>>> 
>>> I am working with the gene dataset in GTF format (the last release, Ensembl81) for Drosophila melanogaster but I have seen that the mod(mdg4)-FBgn0002781 does not exist.
>>> 
>>> Do you know why?
>>> 
>>> Thanks in advance.
>>> 
>>> Cheers,
>>> J
>>> 
>> 
>>