[ensembl-dev] Motif feature consequences discrepancy

[Sigurjón Axel Guðjónsson]

Hi Anja,

Thank you for explaining this.

Would it be possible to optionally show unverified motif features in VEP.  I.e. if the relevant cell line is missing ChIP-Seq peak data.

Best regards,
Sigurjón


From: Dev <dev-bounces at ensembl.org> On Behalf Of Anja Thormann
Sent: fimmtudagur, 12. mars 2020 13:12
To: Ensembl developers list <dev at ensembl.org>
Subject: Re: [ensembl-dev] Motif feature consequences discrepancy

Hi Sigurjon,

VEP only reports overlaps with 'experimentally verified’ motif features. Which means those motif features fully overlap with a relevant ChIP-Seq peak. On the website we are still showing overlaps with unverified motif features. This will be updated for next release 100 when we are only going to show overlaps with 'experimentally verified’ motif features. Our blog post<http://www.ensembl.info/2018/10/15/new-ensembl-motif-features/> gives more details on how we report motif features.

Best wishes,
Anja

On 12 Mar 2020, at 12:53, Sigurjón Axel Guðjónsson <Sigurjon.Gudjonsson at decode.is<mailto:Sigurjon.Gudjonsson at decode.is>> wrote:



Hi,



I am using VEP r99 to annotate i.e. rs759323910, and I notice that VEP only annotates MotifFeature ENSM00524563717 (ENSPFM0379).

The web browser does hower annotate 2 MotifFeatures ENSM00524563717 (ENSPFM0588) and ENSM00489900360 (ENSPFM0379).



See:

http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation



Is there any valid reason for this discrepancy or is this a bug in VEP r99?



Best regards,



Sigurjon A. Gudjonsson

Bioinformatics Group

Decode Genetics
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