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

[林琼芬]

Hello Will,
Thanks for you help. I have try the two method you give, but it doesn't
work. Reference allele has no problem, so as "MT". If there have any other
solution？

Best regard!
Lin

2016-07-04 16:25 GMT+08:00 Will McLaren <wm2 at ebi.ac.uk>:

> 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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>>
>>
>
> _______________________________________________
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>


-- 

Arron Lin

BGI Research Institute

Email: qiongfen0 at gmail.com

Beishan Industrial Zone| Yantian  District| Shenzhen 518083
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