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

Thu Jul 7 03:02:52 BST 2016

Dear Will,
Thank you so much. It do help me a lot, I have find out the bug and trying
to solve, thanks!

Best Regard!
Lin

2016-07-06 18:23 GMT+08:00 Will McLaren <wm2 at ebi.ac.uk>:

> The reference allele is incorrect in your input. If you specify
> --check_ref, VEP will warn you that the allele is wrong (and tell you what
> the correct allele is) and ignore that input:
>
> $ echo "MT 4249 . T C" | perl variant_effect_predictor.pl --database
> --force --check_ref
> 2016-07-06 11:18:22 - Reading input from STDIN (or maybe you forgot to
> specify an input file?)...
> 2016-07-06 11:18:22 - Starting...
> 2016-07-06 11:18:22 - Detected format of input file as vcf
>
> WARNING: Specified reference allele T does not match Ensembl reference
> allele C on line 1
> 2016-07-06 11:18:22 - Wrote stats summary to
> variant_effect_output.txt_summary.html
> 2016-07-06 11:18:22 - See variant_effect_output.txt_warnings.txt for
> details of 1 warnings
> 2016-07-06 11:18:22 - Finished!
>
> Here's the HGVS output with the correct input (assuming that the ref/alts
> are switched):
>
> $ echo "MT 4249 . C T" | perl variant_effect_predictor.pl -data -force
> -pick -check_ref -fields HGVSc,HGVSp -o stdout -hgvs | grep -v #
> ENST00000361390.2:c.943C>T      ENSP00000354687.2:p.Pro315Ser
>
> Regards
>
> Will
>
> On 6 July 2016 at 10:38, 林琼芬 <qiongfen0 at gmail.com> wrote:
>
>> 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
>>>>
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
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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
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
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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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