Hello,
I posted in the reason that I couldn't display xyplot.
I found out and had to conclude that gmod_bulk_load_gff3.pl do not
recognized scores in GFF3 file.
I have two GFF3 files. One is general annotations including tilying array as
well as sequence.
the other one is only for tiling array probes.
After loading the first, xyplot displaying tilying array work well.
However, the second one do not display xyplot proper.
I check the loaded GFF3 file by using GFF dump in Gbrowse.
I realized that score was empty with ".".
I try to make several GFF3 file for the second case(tilying array probe).
ChLGX NGS_probe microarray_oligo 1660 2055 . .
.
ID=ChLGX:Probe_1660_2055;Name=ChLGX:Probe_1660_2055
ChLGX NGS_probe region 1660 1713 2 . .
Parent=ChLGX:Probe_1660_2055
ChLGX NGS_probe region 1755 1804 3 . .
Parent=ChLGX:Probe_1660_2055
ChLGX NGS_probe region 1965 2014 1 . .
Parent=ChLGX:Probe_1660_2055
ChLGX NGS_probe region 2005 2055 1 . .
Parent=ChLGX:Probe_1660_2055
ChLGX NGS_probe microarray_oligo 3116 3321 . .
.
ID=ChLGX:Probe_3116_3321;Name=ChLGX:Probe_3116_3321
ChLGX NGS_probe region 3116 3165 1 . .
Parent=ChLGX:Probe_3116_3321
ChLGX NGS_probe region 3261 3321 1 . .
Parent=ChLGX:Probe_3116_3321
ChLGX NGS_probe microarray_oligo 5202 59320 . .
.
ID=ChLGX:Probe_5202_59320;Name=ChLGX:Probe_5202_59320
:
;
and
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
ChLGX NGS_probe oligo 3116 3165 1 . .
Parent=ChLGX:Probe_1660_73163
ChLGX NGS_probe oligo 3261 3321 1 . .
Parent=ChLGX:Probe_1660_73163
:
;
gmod_bulk_load_gff3.pl did not accepted the scores like that:
> here is
empty
ChLGX NGS_probe region 20001 20059 . . .
dbxref=GFF_source%3ANGS_probe;synonym=auto133105;synonym=region-auto133105
ChLGX NGS_probe region 20066 20119 . . .
dbxref=GFF_source%3ANGS_probe;synonym=auto133106;synonym=region-auto133106
ChLGX NGS_probe region 20106 20163 . . .
dbxref=GFF_source%3ANGS_probe;synonym=auto133107;synonym=region-auto133107
ChLGX NGS_probe region 20151 20205 . . .
dbxref=GFF_source%3ANGS_probe;synonym=auto133108;synonym=region-auto133108
ChLGX NGS_probe region 20206 20257 . . .
dbxref=GFF_source%3ANGS_probe;synonym=auto133109;synonym=region-auto133109
ChLGX NGS_probe region 20251 20305 . . .
dbxref=GFF_source%3ANGS_probe;synonym=auto133110;synonym=region-auto133110
Please let me know what is wrong.
Thank you.
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