[biomart-users] Retrieving results containing only the representative gene models

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[biomart-users] Retrieving results containing only the representative gene models

Venura Herath PhD
Hi,

I am wondering is there a way to obtain results for only the representative gene model. 
As an example lets say I want to retrieve all genes codes for a protein that contains Interpro domain  IPR000007 in potato genome using biomart (@ensembel plants), What ever results I am getting contain all transcript IDs but I want only the representative model for each gene (1 transcript  per gene).
Is there a way to overcome the issue?
Thanks in advance.

Venura

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Re: [biomart-users] Retrieving results containing only the representative gene models

Syed Haider-5
Hi Venura,

If you deselect "Transcript Stable ID" and select only gene level attributes e.g. Gene Stable ID, Gene start, Gene end; and then limit the results to "Unique results only" check box; you should get 1 entry per gene.

Best wishes,
Syed

On Sun, 19 May 2019 at 23:57, Venura Herath PhD <[hidden email]> wrote:
Hi,

I am wondering is there a way to obtain results for only the representative gene model. 
As an example lets say I want to retrieve all genes codes for a protein that contains Interpro domain  IPR000007 in potato genome using biomart (@ensembel plants), What ever results I am getting contain all transcript IDs but I want only the representative model for each gene (1 transcript  per gene).
Is there a way to overcome the issue?
Thanks in advance.

Venura

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Re: [biomart-users] Retrieving results containing only the representative gene models

Venura Herath PhD
Thanks a lot Syed. 

On Mon, May 20, 2019 at 3:26 AM Syed Haider <[hidden email]> wrote:
Hi Venura,

If you deselect "Transcript Stable ID" and select only gene level attributes e.g. Gene Stable ID, Gene start, Gene end; and then limit the results to "Unique results only" check box; you should get 1 entry per gene.

Best wishes,
Syed

On Sun, 19 May 2019 at 23:57, Venura Herath PhD <[hidden email]> wrote:
Hi,

I am wondering is there a way to obtain results for only the representative gene model. 
As an example lets say I want to retrieve all genes codes for a protein that contains Interpro domain  IPR000007 in potato genome using biomart (@ensembel plants), What ever results I am getting contain all transcript IDs but I want only the representative model for each gene (1 transcript  per gene).
Is there a way to overcome the issue?
Thanks in advance.

Venura

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Venura Herath PhD
Department of Agricultural Biology,
Faculty of Agriculture,
University of Peradeniya,
Peradeniya, 
Sri Lanka 20400

"Science is a wonderful thing if one does not have to earn one's living at it."
..Einstein

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