projectionplugin

A JBrowse plugin for re-mapping coordinates "on the fly". Should be considered experimental. Only reverse complement works moderately well

Options

• storeClass - The projections are implemented as store classes which depend on the data types. This plugin currently allows:
  • reverse projections
    • ProjectionPlugin/Store/SeqFeature/ReverseSequence
    • ProjectionPlugin/Store/SeqFeature/ReverseNCList
    • ProjectionPlugin/Store/SeqFeature/ReverseBigWig
    • ProjectionPlugin/Store/SeqFeature/ReverseBAM
  • "folded" regions
    • ProjectionPlugin/Store/SeqFeature/FoldSequence*
    • ProjectionPlugin/Store/SeqFeature/FoldNCList
    • ProjectionPlugin/Store/SeqFeature/FoldBigWig*
    • ProjectionPlugin/Store/SeqFeature/FoldBAM*
  • multiple scaffolds
    • ProjectionPlugin/Store/SeqFeature/ProjectionSequence
    • ProjectionPlugin/Store/SeqFeature/ProjectionNCList
    • ProjectionPlugin/Store/SeqFeature/ProjectionBigWig
    • ProjectionPlugin/Store/SeqFeature/ProjectionBAM*

*denotes in-progress

Screenshots

Example with reverse projection

Config

• reverseComplement - A boolean to specify reverse complementing. This can also be toggled via a menu option that is added when you load the plugin

Example with multi-scaffold projection

Config

"projectionStruct":[{
    "start":0,
    "end":1382403,
    "length":1382403,
    "name": "Group1.1"
},
{
    "start":0,
    "end":1227296,
    "length":1227296,
    "name": "Group1.15"
},
{
    "start":0,
    "end":2277954,
    "length":2277954,
    "name": "Group13.7"
}],

Example with a "folded" region (take away intron)

Config

"foldStruct":{
    "start": 385000,
    "end": 503000,
    "subfeats": [{
       "start": 385000,
       "end": 396500
    },{
       "start":500000,
       "end": 503000
    }]
}

How to use

• Download the plugin to the plugins folder
• Add "plugins": ["ProjectionPlugin"] to your config, or similar
• Supply the storeClass for a reverse projection, folded track, or projection track to your track

Extra notes

• The projection plugin can also be readily combined with SashimiPlot and GCContent plugins
• The useAsRefSeqStore is used on the SequenceTrack to make it a "primary" refseq
• It is planned to make "combinations" of transformations too