[galaxy-user] Fwd: To get the gene name from BED file

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[galaxy-user] Fwd: To get the gene name from BED file

Anton Nekrutenko


Begin forwarded message:

From: Shibu John <[hidden email]>
Date: May 24, 2010 8:25:35 AM EDT
To: Anton Nekrutenko <[hidden email]>
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 <[hidden email]> wrote:
Shibu:

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

Tx,

anton
galaxy team





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Re: [galaxy-user] Fwd: To get the gene name from BED file

Anton Nekrutenko
Shibu:

Upload coordinates of genes from the UCSC Table Browser and intersect them with exome regions as explained in this screencast:


Thanks for using Galaxy!

anton


On May 24, 2010, at 9:29 AM, Anton Nekrutenko wrote:



Begin forwarded message:

From: Shibu John <[hidden email]>
Date: May 24, 2010 8:25:35 AM EDT
To: Anton Nekrutenko <[hidden email]>
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 <[hidden email]> wrote:
Shibu:

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

Tx,

anton
galaxy team




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Re: [galaxy-user] Fwd: To get the gene name from BED file

Andre Pitaluga
Hi,
Does anybody know how to parser the out put of Megablast on 454 data?
I ran the magablast, save it in xml and zip it as requested. After the upload, the parser give this result: "An error occurred running this job: The zipped uploaded file contains inappropriate content"

Any ideas?

Thanks,
André Pitaluga

QUER NAVERGAR COM MAIS SEGURANÇA? VEJA AS DICAS DO INTERNET EXPLORER 8.
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[galaxy-user] MegaBlast Parser

Andre Pitaluga

Hi,
Does anybody know how to parser the out put of Megablast on 454 data?
I ran the magablast, save it in xml and zip it as requested. After the upload, the parser give this result: "An error occurred running this job: The zipped uploaded file contains inappropriate content"

Any ideas?

Thanks,
André Pitaluga

EM 2009 ACONTECERAM 250.362 FRAUDES NA INTERNET. CLIQUE PARA LER DICAS DE SEGURANÇA.
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