Splicing Junctions

Supported file format

The file format for junctions handled by RNAseqViewer is the same as the output junctions.bed computed by the RNA mapper TopHat, i.e. a special form of BED format. Each line of the BED file describes a junction and “consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.” [1]


RNAseqViewer can display the junctions in two alternative types of view: Broken Line View and Bar View.

Broken Line View

The Broken Line View displays the junctions in the usual way, i.e. as lambda-shape broken lines. The color of the lines depends on the number of reads mapped to the junction. The number is also given in a tool tip when your cursor hovers over a junction.

Bar View

The bar view is very close to the way BED Tracks are usually displayed, except for the color which is derived from the number of matching reads like for the Broken Line View.


The screenshot shows one annotation track (hg18) and two identical junction tracks, in Broken Line View (top) and Bar View (bottom).


This figure is shows the same tracks at higher zoom level.