Do the motifs show up if you zoom in?
The motifs should show up, assuming that:
1. you have "subfeatures": true and "subfeature_classes" in your config
file, like this:
"subfeatures": true,
"subfeature_classes": {
"motif1_small_a": "small_red",
"motif1_small_b": "small_blue",
"motif1_small_c": "small_purple",
"motif1_tall_a": "tall_blue",
"motif1_tall_b": "tall_purple"
}
and 2. /var/www/genome.css has a listing for all of the values in the
"subfeature_classes" setting.
If have both of those things, then my best guess for what's going on is
this: by default, subfeatures like your motifs are only shown once you
zoom in beyond a certain level.
The threshold where they show up is controlled by the "subfeatureScale"
setting in the "clientConfig" part of the config file, so you can add
something like this:
"clientConfig": {
"subfeatureScale": 40
},
The default is 80, and if you want the subfeatures to still show up when
you're more zoomed out, set it lower.
The actual units for the "subfeatureScale" setting are pixels/feature.
That value is multiplied by the average feature density in features/base
units (i.e., the number of features in the track / the refseq length) to
get the scale threshold in pixels per base. For example, if the
subfeatureScale is 2, and a track has 100 features, then subfeatures
will be shown if you're zoomed in far enough that the entire refseq
would be at least 200 pixels wide.
Hope this helps,
Mitch
On 10/05/2010 02:24 PM, anja wrote:
> Hi Mitch,
>
> when I visit
http://localhost/ then I see the surface of JBrowse and
> the track as a grey line, so no motifs at all... more then before I guess
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