Splice Junction Track

type = 'junction'

File formats#

bed#

The source file for this track is a .bed file. Each row in the .bed file represents a single splice junction. The name field (column #4) is used to encode the following attributes as semicolon separated key-value pairs (GFF3 column 9 format).

Attributes:

• motif - one of 'GT/AG', 'CT/AC', 'GC/AG', 'CT/GC', 'AT/AC', 'GT/AT', 'non-canonical' (from STAR v2.4)
• uniquely_mapped - number of uniquely mapped reads spanning this junction
• multi_mapped - number of non-uniquely mapped reads spanning this junction
• maximum_spliced_alignment_overhang - used as a filter if minSplicedAlignmentOverhang is defined in the track configuration
• annotationed_juncion

This is an example .bed file row:

chr15   92883778    92885514    motif=GT/AG;uniquely_mapped=95;multi_mapped=10;maximum_spliced_alignment_overhang=38;annotated_junction=true    95  +

Here the attributes are taken directly from the STAR v2 aligner *.SJ.out.tab file.

Configuration Options#

General options

config settings for this track fall into 2 categories: Filtering Options determine which splice junctions are shown, while Display Options change how the splice junctions are displayed.

Display Options#

Property	Description	Default
colorBy	Splice junction color. Possible values: "numUniqueReads", "numReads", "isAnnotatedJunction", "strand", "motif"	"numUniqueReads"
colorByNumReadsThreshold	If colorBy is set to "numUniqueReads" or "numReads", junction color will be darker when number of reads > this threshold	5
thicknessBasedOn	Splice junction line thickness. Possible values: "numUniqueReads", "numReads", "isAnnotatedJunction"	"numUniqueReads"
bounceHeightBasedOn	Splice junction curve height. Possible values: "random", "distance", "thickness"	"random"
labelUniqueReadCount	Add unique read counts to splice junction label	true
labelMultiMappedReadCount	Add multi-mapped read counts to splice junction label	true
labelTotalReadCount	Add total read counts to splice junction label	false
labelMotif	Add splice junction motif to its label	false
labelAnnotatedJunction	If defined, this string will be appended to the labels of splice junctions that exist in known gene models (eg. for which annotated_junction=true in the .bed file). Example value: " [A]"	null
minSplicedAlignmentOverhang		null

Filtering Options#

Property	Description	Default
minUniquelyMappedReads	Junction must be supported by at least this many uniquely-mapped reads.	0
minTotalReads	Junction must be supported by at least this many uniquely-mapped + multi-mapped reads.	0
maxFractionMultiMappedReads	(uniquely-mapped reads)/(total reads) must be <= this threshold	1
minSplicedAlignmentOverhang	Mininum spliced alignment overhang in base pairs. See STAR aligner docs for more details.	0
hideStrand	Set to "+" or "-" to hide junctions on the plus or minus strand.	null
hideAnnotatedJunctions	If true, only novel junctions will be shown (eg. those not found in gene models passed to the aligner)	false
hideUnannotatedJunctions	If true, only annotated junctions will be shown (eg. those found in gene models passed to the aligner)	false
hideMotifs	A list of strings for motif values to hide. For example: ['GT/AT', 'non-canonical']	[]

Example#

{
    type: 'spliceJunctions',
    format: 'bed',
    url: `${rootUrl}/${prefix}.SJ.out.bed.gz`,
    indexURL: `${rootUrl}/${prefix}.SJ.out.bed.gz.tbi`,
    minUniquelyMappedReads: 1,
    minTotalReads: 1,
    maxFractionMultiMappedReads: 1,
    minSplicedAlignmentOverhang: 0,
    thicknessBasedOn: 'numUniqueReads', //options: numUniqueReads (default), numReads, isAnnotatedJunction
    bounceHeightBasedOn: 'random', //options: random (default), distance, thickness
    colorBy: 'isAnnotatedJunction', //options: numUniqueReads (default), numReads, isAnnotatedJunction, strand, motif
    labelUniqueReadCount: true,
    labelMultiMappedReadCount: true,
    labelTotalReadCount: false,
    labelMotif: false,
    labelAnnotatedJunction: " [A]",
    hideStrand: '-',
    hideAnnotatedJunctions: false,
    hideUnannotatedJunctions: false,
    hideMotifs: ['GT/AT', 'non-canonical'], //options: 'GT/AG', 'CT/AC', 'GC/AG', 'CT/GC', 'AT/AC', 'GT/AT', 'non-canonical',
},

Sashimi track: combine 'spliceJunctions' track with 'wig' track#

The 'merged' track type allows a 'spliceJunctions' track to be rendered on top of a 'wig' track to create a full sashimi-like track.

Besides the .bed.gz file described above, this also requires a separate .bigWig file.

{
        type: 'merged',
        name: prefix,
        height: 150,
        tracks: [
          {
            type: 'wig',
            format: "bigwig",
            url: `${rootUrl}/${prefix}.bigWig`,
          },
          {
            type: 'spliceJunctions',
            format: 'bed',
            url: `${rootUrl}/${prefix}.SJ.out.bed.gz`,
            indexURL: `${rootUrl}/${prefix}.SJ.out.bed.gz.tbi`,
        minUniquelyMappedReads: 1,
        ...
          },
        ],
      }