[ensembl-dev] different between eGenetics and GNF/Atlas

[Will McLaren]

Hello Lin,

There is a problem with your input - the reference allele that you have
specified does not match the reference genome sequence. You can have VEP
check your input for this issue by adding --check_ref to your command line.

You should also use "MT" to refer to the mitochondrial chromosome in place
of "M".

Regards

Will McLaren
Ensembl Variation

On 4 July 2016 at 03:53, qiongfen0 at gmail.com <qiongfen0 at gmail.com> wrote:

> Dear Thomas,
> Thanks for your reply, it has help me so much.
> Now, I have another confused, I hope you can help me understand this.
> I am using ensembl-tools-release-77 now, when I use VEP to annotate the
> variants in mitochondria, some has the result of HGVSp but not have HGVSc
> (like the follow printscreen), it may be quiet strange. Then I use the
> VEP online  to try again, but it has no result of HGVSc and HGVSp. I
> wonder what make this result appear.
>
>
> Hope to hear form you.
>
> Yours sincerely,
> Lin
>
> *From:* Thomas Maurel <maurel at ebi.ac.uk>
> *Date:* 2016-06-28 17:30
> *To:* Ensembl developers list <dev at ensembl.org>
> *Subject:* Re: [ensembl-dev] different between eGenetics and GNF/Atlas
> Dear Lin,
>
> I am afraid that this data was retired in Ensembl release 76. These might
> not match as the data is coming from two different sources:
>
> GNF/Atlas data came to us via the Gene Expression Atlas project at
> EMBL-EBI.
>
> http://www.ebi.ac.uk/gxa/
>
> The GNF/Atlas data was published by the Genomics Institute of the Novartis
> Research Foundation:
>
> http://www.gnf.org/technology/organismal/gene-expression-core.htm
>
> The eGenetics database uses Expressed Sequence Tags (ESTs) annotated with
> eVOC ontology terms by SANBI (South African National Bioinformatics
> Institute). More information below.
>
> http://www.ncbi.nlm.nih.gov/pubmed/12799354
> http://www.sanbi.ac.za/
>
> Hope this helps,
> Best Regards,
> Thomas
>
> On 28 Jun 2016, at 03:04, qiongfen0 at gmail.com wrote:
>
> Dear Sirs,
> I'm using biomart to filter a series of genes which are specifically
> expressed in the brain. In biomart there are two such filters,
> 'eGenetics/SANBI EST anatomical system data' and 'GNF/Atlas organism part',
> however, the results of these two filters don't match. I searched for it at
> biomart help but i couldn't find anything about this. Can anybody help me
> to understand the difference of these two filters?
> I am looking forward to hearing from you.
>
> Yours sincerely,
> Lin
>
> Qiongfen Lin
> South China Normal University
> TEL: +8615118845463| Mail : qiongfen0 at gmail.com
>
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>
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
>
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