[galaxy-user] Annotation tool for prokaryotic genome
Hello Galaxy community, I would like to know if there is any available tool in Galaxy for automated gene annotation. I need gene annotation in GTF or GFF3 format to run CuffDiff on a RNA-Seq project that we are. If not, do you recommend me any software or utility. We have the genome annotated in GenBank format, but searching in the web I've seen that is not possible to convert GenBank format to GTF or GFF3. I appreciate your opinions. Thank you, Bernardo -- *Bernardo Bello Ortí* Becario predoctoral FPI CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona) Tel.: 647 42 52 63 *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/
[galaxy-user] Pipeline design for bacterial RNA-Seq
Hi community, I have just discovered a wonderful Galaxy server for RNA-Seq analysis: Oqtans http://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 * * * ___ 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] Search software on public Galaxy servers
Hi community, Due to the increasing Galaxy public servers PublicGalaxyServershttp://wiki.galaxyproject.org/PublicGalaxyServers it would be very useful to have a search tool in order to look for software ready-to-use in the public servers. Since I know this is not available. Will it be feasible? 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 * * * ___ 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/
