Hi, I am still figuring out why my xyplot doesn't work. After loading the tiling probe data file by using gmod_bulk_load_gff3.pl, I realized that the score column was empty,"." rather than a value that my gff3 file assigned.
I 'd like to know if gmod_bulk_load_gff3.pl has a restriction for the score field. Please let me know. Thank you. Hee Shin heekim wrote: > > 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 > -- View this message in context: http://www.nabble.com/one-of-xyplots-has-a-Problem-on-GFF3-with-Chado-tp15598184p15620514.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
