Dr. Gilber,
Thank you for your consideration.
Isabelle, one of GBROWSE users, informed me how to figure out this issue
before you let me know.
All of you pointed out --analysis option.
I followed her direction,
insert into analysis (name,program,programversion)
values('NGS_probe','Gmap','NGS');
then
I ran /usr/local/bin/gmod_bulk_load_gff3.pl --dbname BeetleBaseTest
--organism beetle --gfffile tcas3_ChrLGX_probe.gff3 --analysis NGS_probe
it worked well.
I would like to point out that I thought that the option seemed to be used
for some special features such as match or EST_match. If I don't use the
option for the features, gmod_bulk_load_gff3.pl stops running process then
display its error message.
Unlikely, in my case, gmod_bulk_load_gff3.pl do not provide the error
message. It was so difficult to find out what was wrong. I never recognized
that I have to use the analysis option.
Thank you for all of you.
Hee Shin
Don Gilbert-6 wrote:
>
>
> Hee Shin,
>
>
> Here is a suggestion, if you haven't tried it. Be warned that I haven't
> tried it.
> Using these load options:
> gmod_bulk_load_gff3.pl --analysis=NimbleScan.dataset1 NimbleScan.gff3
> gmod_bulk_load_gff3.pl --analysis=NGS_probe.dataset1 NGS_probe.gff3
>
> should load the data to chado analysisfeatures with these columns:
> table analysis.program=NimbleScan, .source=dataset1
> table analysis.program=NGS_probe, .source=dataset1
> table analysisfeature.significance=GFF.score
>
> and the gbrowse chado adaptor should then find feature.score from
> analysisfeature.significance column.
>
> This may also change the GFF feature.source values for gbrowse.conf
> (I'm not sure):
> > feature = microarray_oligo:NimbleScan.dataset1
> > feature = region:NGS_probe.dataset1
>
> You don't need to add the .dataset1 source name for the analysis. But
> that would be good practice in case you want to add
> NimbleScan.dataset2, .dataset3, etc.
>
>
> - Don
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- [EMAIL PROTECTED]://marmot.bio.indiana.edu/
>
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