Add Tribolium Genome

4.6 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Brenda, The examples below are labeled by the tool/user interface location where the two menus are located. Which tool are you using under "Get Data"? Perhaps "UCSC Main"? Any tool other than "Upload File" accesses an external data source and the available data can vary. It is important to know that the data content included on externally hosted sites is managed by that sites owners. If you are using "Get Data -> UCSC Main", then you are correct in that they do not provide data for this genome, just the ones you list. When you do locate data for this species that you wish you use (try searching for "Tribolium castaneum" with the tool " EBI SRA ENA SRA"), and import it, the Galaxy locally cached reference genome for Tcas_3.0 is available with several, but not all, mapping tools. It is likely to be added to Bowtie2/Tophat2 sometime in the future. Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks-found it! We have a lot of data, but are trying to convert some data to BED format, and I think that this will help. Brenda Hi Brenda, The examples below are labeled by the tool/user interface location where the two menus are located. Which tool are you using under "Get Data"? Perhaps "UCSC Main"? Any tool other than "Upload File" accesses an external data source and the available data can vary. It is important to know that the data content included on externally hosted sites is managed by that sites owners. If you are using "Get Data -> UCSC Main", then you are correct in that they do not provide data for this genome, just the ones you list. When you do locate data for this species that you wish you use (try searching for "Tribolium castaneum" with the tool " EBI SRA ENA SRA"), and import it, the Galaxy locally cached reference genome for Tcas_3.0 is available with several, but not all, mapping tools. It is likely to be added to Bowtie2/Tophat2 sometime in the future. Thanks! Jen Galaxy team Hi Jen, When I go to "get data" and I put "insect" the only pull downs are some Drosophila and Anopheles spp. Is it somewhere else? Thanks, Brenda ________________________________ To: Brenda Oppert; galaxy-user@lists.bx.psu.edu<mailto:galaxy- user@lists.bx.psu.edu=""> Subject: Re: [galaxy-user] Add Tribolium genome Hello Brenda, Are you working at http://usegalaxy.org<http: usegalaxy.org=""/>? I just checked and it is still there. Please give this another look. Thanks! Jen Galaxy team On "Get Data -> Upload File" tool: <mail attachment.png=""> Under "Edit Attributes" (found by clicking on a dataset's pencil icon): <mail attachment.png=""> I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it. Can it be added? Thanks, Brenda ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http: 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org<http: galaxyproject.org=""/> -- Jennifer Hillman-Jackson http://galaxyproject.org<http: galaxyproject.org=""/>

ADD REPLY • link written 4.6 years ago by Brenda Oppert • 20

Similar posts • Search »