BED Tracks

Supported file format

You cane visualize data in BED format. The format is described by UCSC: BED Format. The twelve columns of the format are taken into account by RNAseqViewer, although only the three first ones are mandatory (chrom, chromStart and chromEnd).

Like Genome Annotations, BED tracks can be displayed with two alternative types of view: Collapse View and Expanded View.

Collapse View

The Collapse View shows all the annotations on the same line. Thick lines represent exons and thin lines represent introns. The name is shown under the line and the other data are shown in a tool tip when hovering over the annotation or the name.

Expanded View

The Expanded View shows the annotations on several lines so as to avoid them to collapse.

../../_images/bed.png

The program displays the same BED track twice. The upper track shows the Collapse View and the lower track shows the Expanded View. The track is one of the examples provided by UCSC:

chr7  127471196  127472363  Pos1  0  +  127471196  127472363  255,0,0
chr7  127472363  127473530  Pos2  0  +  127472363  127473530  255,0,0
chr7  127473530  127474697  Pos3  0  +  127473530  127474697  255,0,0
chr7  127474697  127475864  Pos4  0  +  127474697  127475864  255,0,0
chr7  127475864  127477031  Neg1  0  -  127475864  127477031  0,0,255
chr7  127477031  127478198  Neg2  0  -  127477031  127478198  0,0,255
chr7  127478198  127479365  Neg3  0  -  127478198  127479365  0,0,255
chr7  127479365  127480532  Pos5  0  +  127479365  127480532  255,0,0
chr7  127480532  127481699  Neg4  0  -  127480532  127481699  0,0,255