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Old 08-06-2014, 03:37 PM   #1
adrian
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Default 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
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Old 08-06-2014, 11:59 PM   #2
a.kmg
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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.
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Old 08-07-2014, 04:42 AM   #3
adrian
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thank you. it was helpful
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Old 08-07-2014, 05:16 AM   #4
a.kmg
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You're welcome
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