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scaffolds.gff3
by raul petrin
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Hello All
I have one file with 4000 scaffolds and i'm putting into gff3 format. Do I need to create one file for each scaffold_number or can I put all these scaffolds into the same file? If possible put all these scaffolds_number in one file, how can I do this? file1 ##gff-version 3 #sequence-region scaffold_1 1 1965746 scaffold_1 early_female microarray_oligo 1 1965746 . . . ID=early_female;Name=early_female scaffold_1 early_female region 8 57 815.56 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 36 85 405.56 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 60 109 509.56 . . Parent=early_female;Note=scaffold_1 file2 ##gff-version 3 #sequence-region scaffold_256 1 40797 scaffold_256 early_female microarray_oligo 9 40797 . . . ID=early_female;Name=early_female scaffold_256 early_female region 9 61 416.44 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 29 82 503.67 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 64 116 380.56 . . Parent=early_female;Note=scaffold_256 . . file 4000 scaffold_4000 . . . . . . . . Thanks a lot Raul ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: scaffolds.gff3
by Scott Cain-4
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Hi Raul,
Yes, you can put all of the scaffolds in one file. For the sequence-region directive you need to pound signs in front of it, like this: ##sequence-region scaffold_1 1 1965746 Scott On Fri, Nov 6, 2009 at 10:05 PM, raul petrin <rjpetrin@...> wrote: > Hello All > I have one file with 4000 scaffolds and i'm putting into gff3 format. > Do I need to create one file for each scaffold_number or can I put all these > scaffolds into the same file? > If possible put all these scaffolds_number in one file, how can I do this? > > file1 > ##gff-version 3 > #sequence-region scaffold_1 1 1965746 > scaffold_1 early_female microarray_oligo 1 1965746 . . > . ID=early_female;Name=early_female > scaffold_1 early_female region 8 57 815.56 . . > Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 36 85 405.56 . . > Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 60 109 509.56 . . > Parent=early_female;Note=scaffold_1 > > file2 > ##gff-version 3 > #sequence-region scaffold_256 1 40797 > scaffold_256 early_female microarray_oligo 9 40797 . . > . ID=early_female;Name=early_female > scaffold_256 early_female region 9 61 416.44 . . > Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 29 82 503.67 . . > Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 64 116 380.56 . . > Parent=early_female;Note=scaffold_256 > > . > . > file 4000 > scaffold_4000 . . . . . . . . > > > > Thanks a lot > Raul > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Missing files in GBrowse2 SVN repository
by zph
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...
Checking whether your kit is complete... WARNING: the following files are missing in your kit: INSTALL.SKIP lib/Bio/Graphics/Browser2/CAlign.c lib/Bio/Graphics/Browser2/CAlign.pm lib/Bio/Graphics/Browser2/CAlign.xs Please inform the author. ... ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Missing files in GBrowse2 SVN repository
by Lincoln Stein-3
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Sorry. This is now fixed.
Lincoln On Mon, Nov 9, 2009 at 7:05 AM, <zph@...> wrote: ... -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: scaffolds.gff3
by raul petrin
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Hello Scott
Thanks for your answer. Question 1: but I still having problem. This is my file: test.gff3 ##gff-version 3 ##sequence-region scaffold_1 1 258 scaffold_1 early_female microarray_oligo 1 258 . . . ID=early_female;Name=early_female scaffold_1 early_female region 8 57 815.56 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 36 85 405.56 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 60 109 509.56 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 85 134 356.89 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 122 171 579.22 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 145 194 1367.44 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 169 220 838.33 . . Parent=early_female;Note=scaffold_1 scaffold_1 early_female region 201 258 999.44 . . Parent=early_female;Note=scaffold_1 ##sequence-region scaffold_256 1 190 scaffold_256 early_female microarray_oligo 9 190 . . . ID=early_female;Name=early_female scaffold_256 early_female region 9 61 416.44 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 29 82 503.67 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 64 116 380.56 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 92 141 448.56 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 113 166 549.22 . . Parent=early_female;Note=scaffold_256 scaffold_256 early_female region 141 190 437.44 . . Parent=early_female;Note=scaffold_256 When I'm loadind this file into my mysql db, I have no problems, but I can see just scaffold_1 data. If I load scaffold_1.gff3 and scaffold_256.gff3 I can see all data (scaffold_1 and scaffold_256). Question 2: When I open my gbrowse, my Scroll/Zoom always goes to 3.167mbps, and I need to select 50kbps to see my data. How can I put this value default? this is my option in my testfile.conf # max and default segment sizes for detailed view max segment = 50000 default segment = 5000 Thanks again. Raul On Sat, Nov 7, 2009 at 8:00 AM, Scott Cain <scott@...> wrote: Hi Raul, ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: scaffolds.gff3
by Scott Cain-4
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Hi Raul,
You can't reuse the ID 'early_female' for different features. The ID has to be unique for a given feature, and since these are on separate sequences, they are different features. Scott PS: I nearly missed question 2; it's always a bad idea to put two unrelated questions in an email :-) I think what you need is the "initial landmark" option, but I'm not sure from your description. See: http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Appearance_Options for more info. On Nov 9, 2009, at 11:06 AM, raul petrin wrote: > Hello Scott > Thanks for your answer. > Question 1: but I still having problem. > This is my file: test.gff3 > > ##gff-version 3 > ##sequence-region scaffold_1 1 258 > scaffold_1 early_female microarray_oligo 1 > 258 . . . ID=early_female;Name=early_female > scaffold_1 early_female region 8 57 > 815.56 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 36 85 > 405.56 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 60 109 > 509.56 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 85 134 > 356.89 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 122 171 > 579.22 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 145 194 > 1367.44 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 169 220 > 838.33 . . Parent=early_female;Note=scaffold_1 > scaffold_1 early_female region 201 258 > 999.44 . . Parent=early_female;Note=scaffold_1 > ##sequence-region scaffold_256 1 190 > scaffold_256 early_female microarray_oligo 9 > 190 . . . ID=early_female;Name=early_female > scaffold_256 early_female region 9 61 > 416.44 . . Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 29 82 > 503.67 . . Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 64 116 > 380.56 . . Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 92 141 > 448.56 . . Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 113 166 > 549.22 . . Parent=early_female;Note=scaffold_256 > scaffold_256 early_female region 141 190 > 437.44 . . Parent=early_female;Note=scaffold_256 > > When I'm loadind this file into my mysql db, I have no problems, but > I can see just scaffold_1 data. If I load scaffold_1.gff3 and > scaffold_256.gff3 I can see all data (scaffold_1 and scaffold_256). > > Question 2: > When I open my gbrowse, my Scroll/Zoom > always goes to 3.167mbps, and I need to select 50kbps to see my > data. How can I put this value default? > this is my option in my testfile.conf > > # max and default segment sizes for detailed view > max segment = 50000 > default segment = 5000 > > Thanks again. > Raul > > > On Sat, Nov 7, 2009 at 8:00 AM, Scott Cain <scott@...> > wrote: > Hi Raul, > > Yes, you can put all of the scaffolds in one file. For the > sequence-region directive you need to pound signs in front of it, like > this: > > ##sequence-region scaffold_1 1 1965746 > > Scott > > > On Fri, Nov 6, 2009 at 10:05 PM, raul petrin <rjpetrin@...> > wrote: > > Hello All > > I have one file with 4000 scaffolds and i'm putting into gff3 > format. > > Do I need to create one file for each scaffold_number or can I put > all these > > scaffolds into the same file? > > If possible put all these scaffolds_number in one file, how can I > do this? > > > > file1 > > ##gff-version 3 > > #sequence-region scaffold_1 1 1965746 > > scaffold_1 early_female microarray_oligo 1 > 1965746 . . > > . ID=early_female;Name=early_female > > scaffold_1 early_female region 8 57 815.56 . . > > Parent=early_female;Note=scaffold_1 > > scaffold_1 early_female region 36 85 405.56 . . > > Parent=early_female;Note=scaffold_1 > > scaffold_1 early_female region 60 109 > 509.56 . . > > Parent=early_female;Note=scaffold_1 > > > > file2 > > ##gff-version 3 > > #sequence-region scaffold_256 1 40797 > > scaffold_256 early_female microarray_oligo 9 > 40797 . . > > . ID=early_female;Name=early_female > > scaffold_256 early_female region 9 61 > 416.44 . . > > Parent=early_female;Note=scaffold_256 > > scaffold_256 early_female region 29 82 > 503.67 . . > > Parent=early_female;Note=scaffold_256 > > scaffold_256 early_female region 64 116 > 380.56 . . > > Parent=early_female;Note=scaffold_256 > > > > . > > . > > file 4000 > > scaffold_4000 . . . . . . . . > > > > > > > > Thanks a lot > > Raul > > > > > > > ------------------------------------------------------------------------------ > > Let Crystal Reports handle the reporting - Free Crystal Reports > 2008 30-Day > > trial. Simplify your report design, integration and deployment - > and focus > > on > > what you do best, core application coding. Discover what's new with > > Crystal Reports now. http://p.sf.net/sfu/bobj-july > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmod-gbrowse@... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july_______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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