Re: [galaxy-user] Pipeline design for bacterial RNA-Seq
Hi Bernardo, The MLB Galaxy Support Team that runs this Galaxy site asks that they be contacted at: gal...@raetschlab.org (Noted on main home page and listed under Help - Email). They would be the best experts to help you understand and use the tools they have developed. More link/information to their project is in our wiki (http://wiki.galaxyproject.org/PublicGalaxyServers - Oqtans), but starting with this specific project's support email as a first step would be a good choice to get oriented. Good luck with your project! Jen Galaxy team On 12/29/12 2:49 AM, Bernardo Bello wrote: Hi community, I have just discovered a wonderful Galaxy server for RNA-Seq analysis: Oqtanshttp://galaxy.raetschlab.org/. I am impressed by the huge quantity of useful tools that they have integrated there. I'm dealing with bacterial transcriptome analysis. We have the genome sequence of this bacteria. RNA samples are now been sequenced and I am designing a pipeline for data analysis. I would like you to suggest me the tools that I can/should use in order to analyse my data. My sequences come from Ion Torrent platform. For each sample I have a fastQ file of about 3 million sequences. They are less than 200 bp and have a mean of 150 bp. I you need more information please ask me. Thank you very much for your help. Regards, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es http://www.cresa.es * * * ___ 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://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/
Re: [galaxy-user] incompatible frame
Hi Barbara, You are running the analysis at the Cistrome Galaxy instance at http://cistrome.org? I can duplicate the issue with a small test. If the zip file of the dataset is downloaded, unzipped, then opened in a browser (Safari Firefox are the ones I tested), the output seems fine, motifs found or not. I saw some activity about a known display issue with a related tool back in Feb of 2011 in the Cistrome google groups archives, but cannot confirm that this is actually related (making it known). The release notes have an update to this same tool in Dec 2011, which makes me think not. It is also possible that I missed another thread where this was discussed. The best action is to contact the team directly so that they can help. On the top menu bar of the browser is the Help - Cistrome Google Group link. The lab could also be contacted - scroll to bottom of home page. (The link Help - Galaxy QA should not be used at this time). Sorry that you are having problems, but hopefully this will lead to a solution! Best, Jen Galaxy team On 12/27/12 8:18 AM, Barbara Bryant wrote: I’m having trouble viewing SeqPos output; I get “Please use a frames compatible browser when viewing this output” – yet I can see other frames in the browsers. Tried IE, Chrome, Firefox. Any suggestions? Thanks! This email message and any attachments are being sent by Constellation Pharmaceuticals, Inc. The information contained in this e-mail message, and any attachments, may contain information that is confidential or privileged. If you are not the intended recipient, any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by return e-mail and destroy all copies of this message and any attachments. Thank you. For more information about Constellation, please visit us at http://www.constellationpharma.com. ___ 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://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/
[galaxy-user] Upload files from filesystem paths
Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ 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/
Re: [galaxy-user] Upload files from filesystem paths
Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ 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/
