#Sequence Views Plugin This is a JBrowse plugin

This plugin allows the user to manually switch between feature/read views and histogram views. Normally, the switch between view styles depends on the zoom level, which can be frustrating.

##Install

For JBrowse 1.11.6+ in the JBrowse/plugins folder, type:
git clone https://github.com/bhofmei/jbplugin-seqview.git SeqViewsPlugin

downloaded the latest release version at releases.
Unzip the downloaded folder, place in JBrowse/plugins, and rename the folder SeqViewsPlugin

##Activate Add this to jbrowse.conf under [GENERAL]:

[ plugins.SeqViewsPlugin ]
location = plugins/SeqViewsPlugin

If that doesn't work, add this to jbrowse_conf.json:

"plugins" : {
    "SeqViewsPlugin" : { "location" : "plugins/SeqViewsPlugin" }
}

Test

Sample data is included in the plugin to test that the plugin is working properly. With URL as the URL path to the JBrowse instance, navigate a web browser to URL/index.html?data=plugins/SeqViewsPlugin/sample_data.

Use

For all track types that are derived from CanvasFeatures tracks, i.e. Alignments2, CanvasFeatures, smAlginments, or HTMLFeatures have additional options in the Display Mode menu for each track.

• Default: switch between features/histograms based on zoom as it normally would
• Features: force track to show features/alignments; once zoomed out too far, it gives a warning to zoom in
• Histograms: force tack to show histogram/coverage view
  • Alignment-like tracks: if no underlying bigwig file with coverage information, gives user a warning
  • Features-like tracks: always computes histograms

This is especially useful for high density RNA-seq tracks when the switch between features and histograms occurs at an incovienent zoom level.