[ensembl-dev] Biomart Genomic Coding Start/End

[Rhoda Kinsella]

Hi Beat,
I'm afraid not as this would involve a partial re-build which takes  
time and the production cycle for the next release has already begun.  
As a workaround, it is possible to get these scores from the Ensembl  
gene mart. See known bugs item here: http://www.ensembl.info/contact-us/known-bugs/ 
. I hope that helps.
Regards
Rhoda


On 24 May 2012, at 09:11, Beat Wolf wrote:

> Will the fixed biomart also include the missing polyphen_score and  
> sift_score? that would be awesome :)
>
> Beat Wolf
>
>  	
> ----- Message d'origine -----
> De: Rhoda Kinsella <rhoda at ebi.ac.uk>
> Date: Thu, 24 May 2012 09:00:18 +0100
> Sujet: Re: [ensembl-dev] Biomart Genomic Coding Start/End
> À: Ensembl developers list <dev at ensembl.org> Hi Simon
> Yes this is likely to be related to the issue below. Can you send me  
> a specific example so that I can check that this? We have rerun the  
> calculations and are in the process of testing to make sure all id  
> okay before copying the fixed mart to the live site. I will send an  
> email once the fix has been made live.
> Regards
> Rhoda
>
> On 23 May 2012, at 18:06, Simon Chan wrote:
>
> Hello,
>
> I'm using BioMart to fetch all protein coding portions of all exons  
> of all transcripts of my favourite gene (Ensembl Genes 67, Homo  
> sapiens genes GRCh37.p7).  In the past, 'Genomic coding start' and  
> 'Genomic coding end' would give me all exon coordinates minus UTRs.   
> However, now it seems to return the UTR coordinates as well.   
> Perhaps this is related to the UTR issue reported by Beat below?
>
> Thank you.
> Simon.
>
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On  
> Behalf Of Rhoda Kinsella
> Sent: Tuesday, May 22, 2012 3:38 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Ensembl release 67 is out!
>
> Hi Beat
> We are currently looking into why this has occurred but it is  
> certainly a bug in our mart databases. I will respond as soon as we  
> have a fix in place. Thank you for reporting this and apologies for  
> any inconvenience.
> Regards
> Rhoda
>
> On 19 May 2012, at 15:55, Beat Wolf wrote:
>
>
> Hi,
>
> i'm a computer scientist and not a biologist, so perhaps i missed  
> something about the DMD gene changing recently.
> I have an automated unit test for my application that uses biomart.  
> It happens to test the DMD-001 transcript of the DMD gene.
> In the 66 version of enembl, the UTR3 coordinates of the exon number  
> 79 where:
>
> 31137345
> to 31140035
> which was correct. Now with the version 67 of ensembl, the UTR3  
> region in the same exon is:
>
> 31137345 to
> 31137344
> Which can not be correct, because that means that UTR3 has a length  
> of 1. The other numbers don't match up either.
>
> Did the DMD gene change? Is the information stored differently in  
> ensembl? What values do i need to reconstruct the true UTR3 region?  
> Or is this a bug in the new ensembl version. If yes, how many other  
> genes are affected? Currently i will stay on the 66 version thanks  
> to the archives, but i have some connection issues with it, it seems  
> to be much less stable than the 67 version.
>
> Greetings
>
> Beat Wolf
>
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>
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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