Supported file format

Transcripts can be visualized in RNAseqViewer in GTF2 format (Gene Transfer Format). Note that GTF is the output format for Cufflinks and RNAseqViewer can read the optional attributes of GTF format produced by Cufflinks, which are described in Cufflinks’s manual.

Collapse View and Expanded View

Like BED Tracks, transcripts can be shown in an expanded view (default) or a collapse view if you want to display transcripts in a more compact way.

In default configuration, the color of the transcripts depends on the FPKM. This can be changed to \log_{10}(\text{FPKM} + 1) or \log_{10}^2(\text{FPKM} + 1) in the track settings (right click on the track).

More information about the transcripts found by Cufflinks are provided in tool tips.


This example shows the transcripts assembled by Cufflinks (lower tracks). For example, the gene CUFF.265 has two isoforms: CUFF.265.1 and CUFF.265.2. The mouse hovers over the transcript CUFF.265.2 and some data about it are shown in a tool tip. The reads and junction reads used by Cufflinks for the assembly are shown in the first two tracks.