Re: [Gmod-ajax] Representation of exons and introns with jbrowse

[Ian H. <ih...@be...>]

Hi Isabelle,

Yes - subfeatures can be used to display exon/intron structure.

The GFF file corresponding to the example config file 'volvox.json' that 
you included (full path docs/tutorial/conf_files/volvox.json) is in 
docs/tutorial/data_files/volvox.gff3. The corresponding sequence file is 
docs/tutorial/data_files/volvox.fa.

There is currently no way to modify the height of a track except by 
hacking the javascript yourself (so, no configuration-level way to do it).

best wishes,
Ian

Isabelle Luyten wrote:
> Hello,
> 
> I am very interested in your tool jbrowse.
> 
> But I am not safe to use all its possibilities.
> 
> I have 2 questions:
> 
> 1)  I want to show exon-intron strucutre of mRNA.
> 
> I ask the same question as Motokazu Ishikawa, but I did not find answer 
> to his question under this site:
> 
> Under http: // mailarchive / forum.php sourceforge.net/? 
> Forum_name=gmod-ajax
>    [ Gmod-ajax ] Subfeature were not shown      Motokazu Ishikawa < 
> m.ishikawa@is >      1      2009-10-16 00:44
> 
> Could I have the file GFF corresponding In the following tracks? 
> (volvox.json)
> 
>     {
>       "track": "CDS",
>       "feature": ["CDS:predicted", "mRNA:exonerate"],
>       "class": "cds",
>       "phase": 1,
>       "key": "Predicted genes",
>       "category": "Genes"
>     },
>     {
>       "track": "Transcript",
>       "feature": ["mRNA:exonerate"],
>       "description": 1,
>       "class": "transcript",
>       "subfeatures": true,
>       "subfeature_classes": {
>         "CDS": "transcript-CDS",
>         "UTR": "transcript-UTR"
>       },
>       "arrowheadClass": "transcript-arrowhead",
>       "key": "Exonerate predictions",
>       "category": "Genes"
>     },
> 
> 
> Do sub-features well serve to display introns and exons for example, or 
> otherwise to which are of use you they?
> 
> 2) I have sometimes 100 in 200 elements for a track (ex ESTs)
> 
> How to decrease the height of these tracks?
> Is it with the NClists?
> Can you give me an example or give me the Web address where I can find it?
> 
> Best regards
>