Begin forwarded message:

From: Shibu John <shibujohn82@gmail.com>

Date: May 24, 2010 8:25:35 AM EDT

To: Anton Nekrutenko <anton@bx.psu.edu>

Subject: To get the gene name from BED file

Hi,
How can I get the gene names for the whole exome locations ( hg18)..

********************
chr1    58932    59892
chr1    357510    358470
chr1    610947    611907
chr1    851160    851280
chr1    855395    855608
chr1    856246    856366
chr1    860956    861196
********************

I used the "Profile Annotations for a set of genomic intervals".. But I am not getting proper output...

I just want the at least gene name in the fourth column for each location..like this
**************************
chr1    58932    59892    OR4F5:ccds|CCDS30547.1
chr1    357510    358470    OR4F16:ccds|CCDS41220.1
chr1    610947    611907    OR4F16:ccds|CCDS41221.1
chr1    851160    851280    SAMD11:ccds|CCDS2.2
chr1    855395    855608   SAMD11:ccds|CCDS2.2
chr1    856246    856366    SAMD11:ccds|CCDS2.2
chr1    860956    861196    SAMD11:ccds|CCDS2.2
******************

Can you help me to get this information from galaxy?

Thanks,
Shibu

On Thu, May 20, 2010 at 2:52 PM, Anton Nekrutenko <anton@bx.psu.edu> wrote:

Shibu:

We experienced disk problems overnight. Galaxy is back to normal.

Tx,

anton
galaxy team

Anton Nekrutenko

http://nekrut.bx.psu.edu

http://usegalaxy.org

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