I loaded the data into Chado through gmod_bulk_load_gff3.pl. I wrote scores in my previous message.
Thank you. Isabelle Blanc-Lenfle wrote: > > Hi, > Do you open your gff files directly with GBrowse or do you load your > data in a database ? > > How are your scores loaded in your database (tilling array different of > probes ?) Is your tiling array data loaded as an analysis and the probes > not ? (case of a chado database). > > Isabelle > > heekim a écrit : >> Hi, >> >> I have a problem with displaying xyplot. >> In my gbrowse, I have two xyplots, one represents tiling array and the >> other >> represents it's probe. >> >> As you can see (please turn on tiling array and tiling array probe) : >> http://129.130.115.71/cgi-bin/gbrowse/BeetleBase3.gff3/?name=ChLGX%3A1303738..1321859 >> >> the tiling array works while it's probe not. >> >> the conf file includes the followings: >> >> [NimbleScan] >> feature = microarray_oligo:NimbleScan >> glyph = xyplot >> graph_type = boxes >> height = 50 >> min_score = 0 >> max_score = 8000 >> scale = left >> fgcolor = blue >> category = genes >> key = Tiling Array >> >> >> [Probes] >> feature = region:NGS_probe >> glyph = xyplot >> graph_type = boxes >> height = 50 >> min_score = 0 >> max_score = 3 >> bump = 0 >> scale = left >> fgcolor = blue >> category = genes >> key = Tiling Array Probe >> >> the GFF files ( I used seperated GFF file for the prob): >> >> ChLGX NimbleScan microarray_oligo 1303738 1391859 . >> . . >> ID=NimbleScan:ChLGX:1303738_1391859;Name=NimbleScan:ChLGX:1303738_1391859 >> ChLGX NimbleScan region 1303738 1303788 3374.78 + 0 >> Name=LG100P000760000;Parent=NimbleScan:ChLGX:1303738_1391859 >> : >> : >> >> This is for the prob: >> >> ChLGX NGS_probe region 1660 73163 . . . >> ID=ChLGX:Probe_1660_73163;Name=ChLGX:Probe_1660_73163 >> ChLGX NGS_probe oligo 1660 1713 2 . . >> Parent=ChLGX:Probe_1660_73163 >> ChLGX NGS_probe oligo 1755 1804 3 . . >> Parent=ChLGX:Probe_1660_73163 >> ChLGX NGS_probe oligo 1965 2014 1 . . >> Parent=ChLGX:Probe_1660_73163 >> ChLGX NGS_probe oligo 2005 2055 1 . . >> Parent=ChLGX:Probe_1660_73163 >> : >> : >> >> I am looking forward to your help again. >> >> Hee Shin > > > -- > Isabelle Blanc-Lenfle > INRA URGI > 523 place des terrasses de l'agora > 91000 Evry - France > > Tel : +33 1 60 87 37 59 > Fax : +33 1 60 87 37 00 > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Gmod-gbrowse mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- View this message in context: http://www.nabble.com/one-of-xyplots-has-a-Problem-on-GFF3-with-Chado-tp15598184p15618694.html Sent from the gmod-gbrowse mailing list archive at Nabble.com. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-gbrowse mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
