Shibu: Upload coordinates of genes from the UCSC Table Browser and intersect them with exome regions as explained in this screencast: http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html Thanks for using Galaxy! anton On May 24, 2010, at 9:29 AM, Anton Nekrutenko wrote:

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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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