Hi Mike,
Jen forgot to mention that you need to change "Group" to "Variation and Repeats", default is "Genes and Gene Prediction".
Please also note that: a) this thread was about mouse, so you need to change "genome" to "human" b) UCSC has dbSNP Build 131 (SNP 131) for human, but the most recent dbSNP build is 133.
HTH, Thomas
On Thu, Apr 7, 2011 at 04:32, Mike Dufault dufaultm@yahoo.com 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:
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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:
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: