gmod-ajax

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

[Isabelle L. <isa...@ve...>]

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

-- 
Isabelle

--------------------------------------
isa...@ve...
INRA-URGI:
Unité de Recherche Génomique Info
Centre de Recherche de Versailles-Grignon
01 30 83 38 30
--------------------------------------

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
> 

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

[Isabelle L. <isa...@ve...>]

Hi Ian,

Thank you,
My configuration file was badly written
Now It's OK
I see exons

best wishes,
Isabelle


Ian Holmes wrote:
> 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
>>


-- 
Isabelle

--------------------------------------
isa...@ve...
INRA-URGI:
Unité de Recherche Génomique Info
Centre de Recherche de Versailles-Grignon
01 30 83 38 30
--------------------------------------