Re: [Gmod-ajax] Jbrowse sub-feature labels

[Michal Č. <mis...@gm...>]

Hello,
thank you for reply. I am happy to attach gff file. This file is than
loaded to Chado using gmod_bulk_load_gff3.pl. More information can be found
here http://gmod.org/wiki/Load_GFF_Into_Chado
I am not sure how to correctly dump all needed information from db. But i
believe, that i am able to config biodb-to-json same way as
flatfile-to-json. I tried what you suggested and result (attached image)
looks promising. However it seems that i can not see subfeatures, just
parent ones.
Sorry about not mentioning the biostar post.

Thanks for your help
Michal Cervenansky

On Wed, 8 Aug 2018 at 16:41, Colin <col...@gm...> wrote:

> Hi there,
>
> It would probably help to have some sort of idea of what type of data is
> being loaded to see what is going on. Generally the easiest way to load
> data is just from a simple GFF3 with flatfile-to-json.pl instead of
> biodb. In this way you can just have a GFF with the parent/child
> relationships specified like gene->mRNA->exon/CDS (both exon and CDS have
> the mRNA as the parent)
>
> Then use
>
> flatfile-to-json.pl --gff features.gff --trackLabel Genes --trackType
> CanvasFeatures
>
> If you do need to use biodb-to-json we might need more details on the
> biodb dataset being used (maybe a small sample data dump and we can help)
>
> Just for cross-reference I think this is a biostars post with the same
> issue  https://www.biostars.org/p/323306/#329722
>
> -Colin
>
> On Sun, Jun 17, 2018 at 8:59 AM Michal Červeňanský <
> mis...@gm...> wrote:
>
>> Dear JBrowse team,
>> I am experiencing difficulties with biodb-to-json.pl configuration file.
>> I would like to use feature - subfeature relationship and using various
>> glyphs the visualization looks okey, but i am not able to see labels, or
>> name tags over the sub-features, i would like them to behave like ordinary
>> features.
>> If i use only ordinary features they are drawn under each other. I would
>> like them to be in one row with sub-features of different color.
>> I would love to have visualization like Volvox CanvasFeatures -
>> Protein-coding gene, but with named sub-features.
>> Can you recommend me how to achieve it ? Any tip would be helpful.
>>
>> Thanks for your help.
>>
>> Regards
>> Michal Červeňanský.
>>
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