Hi,
Is it possible to convert a fasta file to sam/bam format using galaxy. ?
OR
Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast)
Thank you Teja
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
On 5/13/11 2:53 PM, sukeerthi teja Rallapalli wrote:
Hi,
Is it possible to convert a fasta file to sam/bam format using galaxy. ?
OR
Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast)
Thank you Teja
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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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
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
On 5/16/11 12:49 PM, Mike Dufault wrote:
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
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:
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
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
On May 17, 2011, at 1:18 PM, Mike Dufault wrote:
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 ___________________________________________________________ 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:
Hi Dannon,
That was too easy! I wish all issues were that easy to fix.
Thanks, Mike
--- On Tue, 5/17/11, Dannon Baker dannonbaker@me.com wrote:
From: Dannon Baker dannonbaker@me.com 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
On May 17, 2011, at 1:18 PM, Mike Dufault wrote:
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 ___________________________________________________________ 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:
galaxy-user@lists.galaxyproject.org
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Dannon Baker -
Jennifer Jackson -
Mike Dufault -
sukeerthi teja Rallapalli