Re: [galaxy-user] genomic coordinates to Enterz gene ids
Hi Kanwar, Both UCSC and Biomart have this data. So you could use the tools in Get Data, pull over the complete set for the genome, then identify overlapping regions versus your coordinates with the tool Operate on Genomic Intervals - Join. For UCSC, the track is UCSC Genes (the linked table knownToLocusLink has Entrez ID). For Biomart, you can select the Entrez ID from the list of optional fields to include per species (be sure to avoid any long text description fields or you may get an HTML import error, or test and omit if this comes up). UCSC also has an intersection function in their Table Browser. Send the Galaxy dataset over as a custom track then intersect with the UCSC Genes track. The Table browser's user guide has instructions. Hopefully one of these works out for you! Jen Galaxy team On 6/14/13 3:18 PM, shamsher jagat wrote: I have a list of around 3000 genomic coordinates of mouse genome and I would iike to extract gene name Enetrz gene ids Is it possible to extract this information in galaxy. Thanks Kanwar ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
Hi Daquing, No, Galaxy does not work with the data in this format and no tools have been donated to the tool shed by the data format authors to do the conversion. You'll have to convert before loading into Galaxy, but from there it can be prepped using tools in the group FASTQ Manipulation. There are also some mapping tools that use converted SOLiD data as input specifically, these can be used on the Test server https://test.g2.bx.psu.edu/ or a local or cloud Galaxy. http://getgalaxy.org http://usegalaxy.org/cloud Best, Jen Galaxy team On 6/13/13 3:53 PM, Wang, Daqing wrote: Hello, I wonder if Galaxy take SOLiD XSQ format data as input for mapping. I know it takes csfasta/qual data. Does anyone try this kind of analysis with SOLiD XSQ format? Any feedback and advice is appreciate it. Thank you! Daqing Wang** ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
