Question: Regrading Snps
0
gravatar for Nripesh Prasad
7.6 years ago by
Nripesh Prasad10 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
galaxy • 1.0k views
ADD COMMENTlink modified 7.5 years ago by Jennifer Hillman Jackson25k • written 7.6 years ago by Nripesh Prasad10
0
gravatar for Jennifer Hillman Jackson
7.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD COMMENTlink written 7.5 years ago by Jennifer Hillman Jackson25k
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 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 -- 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/
ADD REPLYlink written 7.5 years ago by Mike Dufault270
Hello Again,   Sorry, I did not realize that I needed to also to select Group: Variation and Repeats.   Thanks anyway, Mike 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 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 -- 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/ ___________________________________________________________ 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/
ADD REPLYlink written 7.5 years ago by Mike Dufault270
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD REPLYlink written 7.5 years ago by Jennifer Hillman Jackson25k
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
ADD REPLYlink written 7.5 years ago by Thomas Juettemann10
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