A JBrowse implementation of the sashimi plot style tool. Features a storeclass that converts RNA-seq BAM files into intron support coverage features, a track type that adds menu options, and a featureglyph that draws arcs.
Other options on the BAM store tracks can apply, such as chunkSizeLimit
The test/data directory contains an example config. There are several different setups
Calculate junctions straight from a BAM file with a config like this
{
"label": "Nurse_junctions",
"storeClass": "JBrowse/Store/SeqFeature/BAM",
"type": "SashimiPlot/View/Track/Sashimi",
"urlTemplate": "Nurse.bam",
"chunkSizeLimit": 50000000,
"useXS": true
}
Using a junctions.bed file loaded with flatfile-to-json.pl, example command bin/flatfile-to-json.pl --bed junctions.bed --trackType SashimiPlot/View/Track/Sashimi --trackLabel sashimi_junctions
which will generate a config like this below...shouldn't need any hand editing
{
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"urlTemplate" : "tracks/test/{refseq}/trackData.json",
"type" : "SashimiPlot/View/Track/Sashimi",
"label" : "From_junctions_bed"
}
Using a junctions.bed file with BEDTabix
{
"storeClass" : "JBrowse/Store/SeqFeature/BEDTabix",
"urlTemplate" : "junctions.bed.gz",
"type" : "SashimiPlot/View/Track/Sashimi",
"label" : "From_junctions_bedtabix"
}
Note: junctions.bed files include score and strand, so their behavior will be the same as if you were calculating this from the BAM file. The "Use XS" will simply apply to the bed file strand instead of the BAM file XS tag