Calling Snp'S

7.5 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Teja, If you have a fasta file of sequences, you can map them to a reference genome to obtain a SAM file (which you could then compress into BAM). See the tool section "NGS Toolbox". BLAST is an alignment tool and additional parsing/analysis tools would be needed in order to identify SNPs. If you do your analysis this way, and SNPs are called outside of Galaxy using your own methods, the final output could be converted into a format such as BED. Then Galaxy could be used to perform analysis vs public SNP databases. To locate the SNP tools available Galaxy, in the left pane of the UI, choose "Options -> Show Search Tool" and enter the keyword "SNP". Please let us know if you would like help with any of the tools, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.5 years ago by Jennifer Hillman Jackson ♦ 25k

Dear Galaxy Team, Is there a way to download file >4Gb from the PSU Galaxy server? I have been working with Galaxy both on the PSU server and on the cloud. I know how to download large files (eg BAM) from the cloud by ssh into the instance, but is there a way to get large file from the PSU server? Thanks, Mike

ADD REPLY • link written 7.5 years ago by Mike Dufault • 270

Hello Mike, You can fetch data from the public server using wget or curl. The link to download can be obtained by right clicking the floppy disk icon inside a history item and choosing "Copy Link Address." Once you have the link: % wget '<link>' or % curl -O '<link>' The quotes aren't strictly necessary but will prevent the shell from evaluating the '?' character in the link. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.5 years ago by Jennifer Hillman Jackson ♦ 25k

Dear Galaxy Team, I have created a workflow that I would like to use frequently. I saved the work flow to my desktop as a ".ga" file and I would now like to import it into a new Cloudman Instance. Using a new/blank history, I selected "options" and then selected "import from file." The only option that I get is to "Import History from an Archive" and it wants a URL. How can Import my workflow.ga file so that I can use it future instances of Galaxy? Thanks, Mike

ADD REPLY • link written 7.5 years ago by Mike Dufault • 270

On the workflows landing page you should find an option to "Upload or import workflow" in the top right. Clicking that will allow you to supply a URL to a shared galaxy workflow, or in your case paste in the contents of the .ga file in the "Encoded workflow" box and it should work. Direct file upload of the .ga export will be available at some point. -Dannon

ADD REPLY • link written 7.5 years ago by Dannon Baker ♦ 3.7k

Hi Dannon, That was too easy! I wish all issues were that easy to fix. Thanks, Mike Subject: Re: [galaxy-user] How to load/import saved workflow ".ga" files into Galaxy? To: "Mike Dufault" <dufaultm@yahoo.com> Cc: galaxy-user@lists.bx.psu.edu Date: Tuesday, May 17, 2011, 1:26 PM On the workflows landing page you should find an option to "Upload or import workflow" in the top right. Clicking that will allow you to supply a URL to a shared galaxy workflow, or in your case paste in the contents of the .ga file in the "Encoded workflow" box and it should work. Direct file upload of the .ga export will be available at some point. -Dannon

ADD REPLY • link written 7.5 years ago by Mike Dufault • 270

7.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Teja, Exploring the "Pages" tutorials is recommended as many have SNP- specific analysis examples. I am not sure if your data is RNA or DNA or if you have quality scores available, but there are tutorials that cover most common-use cases. http://main.g2.bx.psu.edu/page/list_published It is recommended to start with these: http://main.g2.bx.psu.edu/u/aun1/p/screencasts http://main.g2.bx.psu.edu/u/james/p/exercises http://main.g2.bx.psu.edu/u/aun1/p/galaxy101 Good luck with your research! Best, Jen Galaxy team ps: For next time, please keep the galaxy-user cc so that our entire team can contribute to replies. This would be especially helpful when you have a new question. -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.5 years ago by Jennifer Hillman Jackson ♦ 25k

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