Getting gene coordinate not exons

adrian · 08-06-2014, 04:37 PM

Hi:
Is there a way to get gene coordinates rather exon coordinates for Hg19 as a bed file.

I do not want exon coordinates since it is repeating my values from a different file.

I want to have:

Chr1 x y Gene1
Chr1 x1 y1 Gene2
chr1 x1 y3 Gene3

Thanks
Adrian

a.kmg · 08-07-2014, 12:59 AM

You can use the Biomart of Ensembl to recover this file.

http://www.ensembl.org/biomart/

Choose your dataset (human, mouse, ...)

Select the attributes you want. Here:

Features => GENE :

Ensembl Gene ID
Gene Start (bp)
Gene End (bp)
Chromosome Name

(clear "Ensembl Transcript ID", which is checked by default)

Click on "Results" and export the data.

adrian · 08-07-2014, 05:42 AM

thank you. it was helpful

a.kmg · 08-07-2014, 06:16 AM

You're welcome

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08-06-2014, 04:37 PM	#1
adrian Member Location: baltimore Join Date: Oct 2009 Posts: 89	Getting gene coordinate not exons Hi: Is there a way to get gene coordinates rather exon coordinates for Hg19 as a bed file. I do not want exon coordinates since it is repeating my values from a different file. I want to have: Chr1 x y Gene1 Chr1 x1 y1 Gene2 chr1 x1 y3 Gene3 Thanks Adrian

08-07-2014, 12:59 AM	#2
a.kmg Member Location: Internet Join Date: Aug 2014 Posts: 15	You can use the Biomart of Ensembl to recover this file. http://www.ensembl.org/biomart/ Choose your dataset (human, mouse, ...) Select the attributes you want. Here: Features => GENE : Ensembl Gene ID Gene Start (bp) Gene End (bp) Chromosome Name (clear "Ensembl Transcript ID", which is checked by default) Click on "Results" and export the data.

08-07-2014, 05:42 AM	#3
adrian Member Location: baltimore Join Date: Oct 2009 Posts: 89	thank you. it was helpful

08-07-2014, 06:16 AM	#4
a.kmg Member Location: Internet Join Date: Aug 2014 Posts: 15	You're welcome