Hello Again,   Sorry, I did not realize that I needed to also to select Group: Variation and Repeats.   Thanks anyway, Mike

--- On Wed, 4/6/11, Mike Dufault dufaultm@yahoo.com wrote:

From: Mike Dufault dufaultm@yahoo.com Subject: Re: [galaxy-user] Regrading SNPs To: "Nripesh Prasad" np0005@uah.edu, "Jennifer Jackson" jen@bx.psu.edu Cc: galaxy-user@lists.bx.psu.edu Date: Wednesday, April 6, 2011, 10:32 PM

Hi Jen,   I tried to follow the directions that you provided, but I don't see "SNP (128)" as a track option. Actually, I am interested in human SNPs and I can not find that either. Do you have any idea if UCSC has removed the track; or am I just looking in the wrong place? Is there anywhere else that to get the data exported for use by Galaxy?   Thanks, Mike

--- On Wed, 4/6/11, Jennifer Jackson jen@bx.psu.edu wrote:

From: Jennifer Jackson jen@bx.psu.edu Subject: Re: [galaxy-user] Regrading SNPs To: "Nripesh Prasad" np0005@uah.edu Cc: galaxy-user@lists.bx.psu.edu Date: Wednesday, April 6, 2011, 4:56 PM

Hello Nripesh,

It is not clear exactly what you want to do, but to get data into Galaxy:

The SNPs from UCSC can be imported using the "Get Data -> UCSC Main" tool. Once the Table browser comes up, select the mouse genome (mm9?), and the track "SNPs (128)". When exporting, make sure the "Galaxy" checkbox is selected.

For your other data, use FTP upload using the "Get Data -> Upload" tool. FTP using a unix terminal or with a desktop client such as FileZilla following the instructions on the tool page. Once the FTP is complete, return to this tool, select the file and load into your history.

Once both files are present, you may need to make some changes to format using "Text Manipulation", depending on what you will do next.

It may help to review some of our tutorials: http://main.g2.bx.psu.edu/page/list_published

And other shared data/workflows, via top menu bar "Shared".

Please let us know if we can help with a specific tool (sharing your history would be helpful "Options -> Share or Publish").

Best,

Jen Galaxy team

On 3/18/11 2:32 PM, Nripesh Prasad wrote:

I wish to compare SNPs in my mouse sample (SNP file generated from Partek Genomic suite) with SNPs from UCSC browser. how do i do that on galaxy? Nripesh Prasad

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-----Inline Attachment Follows-----

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

Hello Mike,

For hg19, the UCSC Table Browser is a source, too. (sounds like you have worked out the query details on the form).

If you are willing to use hg18, then SNPs formatted and ready to use are already in Galaxy under "Shared Data -> Libraries -> Putative SNP phenotypes". You can just check a dataset to load it into your history.

Thanks!

Jen Galaxy team

On 4/6/11 7:32 PM, Mike Dufault wrote:

Hi Jen, I tried to follow the directions that you provided, but I don't see "SNP (128)" as a track option. Actually, I am interested in human SNPs and I can not find that either. Do you have any idea if UCSC has removed the track; or am I just looking in the wrong place? Is there anywhere else that to get the data exported for use by Galaxy? Thanks, Mike

--- On *Wed, 4/6/11, Jennifer Jackson /jen@bx.psu.edu/* wrote:

From: Jennifer Jackson <jen@bx.psu.edu>
Subject: Re: [galaxy-user] Regrading SNPs
To: "Nripesh Prasad" <np0005@uah.edu>
Cc: galaxy-user@lists.bx.psu.edu
Date: Wednesday, April 6, 2011, 4:56 PM

Hello Nripesh,

It is not clear exactly what you want to do, but to get data into
Galaxy:

The SNPs from UCSC can be imported using the "Get Data -> UCSC Main"
tool. Once the Table browser comes up, select the mouse genome
(mm9?), and the track "SNPs (128)". When exporting, make sure the
"Galaxy" checkbox is selected.

For your other data, use FTP upload using the "Get Data -> Upload"
tool. FTP using a unix terminal or with a desktop client such as
FileZilla following the instructions on the tool page. Once the FTP
is complete, return to this tool, select the file and load into your
history.

Once both files are present, you may need to make some changes to
format using "Text Manipulation", depending on what you will do next.

It may help to review some of our tutorials:
http://main.g2.bx.psu.edu/page/list_published

And other shared data/workflows, via top menu bar "Shared".

Please let us know if we can help with a specific tool (sharing your
history would be helpful "Options -> Share or Publish").

Best,

Jen
Galaxy team


On 3/18/11 2:32 PM, Nripesh Prasad wrote:
 > I wish to compare SNPs in my mouse sample (SNP file generated from
 > Partek Genomic suite) with SNPs from UCSC browser. how do i do
that on
 > galaxy?
 > Nripesh Prasad
 >
 >
 >
 > ___________________________________________________________
 > The Galaxy User list should be used for the discussion of
 > Galaxy analysis and other features on the public server
 > at usegalaxy.org. Please keep all replies on the list by
 > using "reply all" in your mail client. For discussion of
 > local Galaxy instances and the Galaxy source code, please
 > use the Galaxy Development list:
 >
 > http://lists.bx.psu.edu/listinfo/galaxy-dev
 >
 > To manage your subscriptions to this and other Galaxy lists,
 > please use the interface at:
 >
 > http://lists.bx.psu.edu/

-- Jennifer Jackson
http://usegalaxy.org <http://usegalaxy.org/>
http://galaxyproject.org <http://galaxyproject.org/>
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/