Hi Seyed, Please always cc the gbrowse mailing list (as I've done here). The GBrowse "not found" message is usually the result of a problem with the GFF, and that problem is usually not having defined the reference sequence in the GFF. In your example, you're looking for a reference sequence called chr20. Is there a line in your GFF that looks something like: chr20 . chromosome 1 1243456788 . . . Name=chr20 where the big number is the length of the feature? The important bit is that the Name attribute match the name in the first column. Scott On Tue, Jun 7, 2016 at 7:24 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
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Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Dear Dr. Cain, Thanks for reply and answering the problem. Yes you are right there is no Name column which equal to chr20, instead it includes Gene name, Ensemble Id or ... for Name field. How can I fix that file in the right way? Please take a look at below chr_20.gff file : You can see also number if GFF lines:
Kind regards, Ahmad On Sat, Jun 11, 2016 at 12:40 AM, Scott Cain <[hidden email]> wrote:
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Hi Ahmad, Like I wrote in my previous email, you need a line in your GFF that identifies chr20 (and any other reference sequences you have), like this: chr20 . chromosome 1 12345678 . . . Name=chr20 You don't have to reload your database with all of the mRNA data, just create a file with these lines in them and load them into the same database. Scott On Sat, Jun 11, 2016 at 6:44 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
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Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Dear Dr. Cain, Many thanks for reply, it just worked.On Sat, Jun 11, 2016 at 6:19 PM, Scott Cain <[hidden email]> wrote:
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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