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Visualize coverage, canonical, and backsplice junctions.
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Visualize coverage, canonical, and backsplice junctions.

Example plot



Example pipeline


This will generate figure 1B and 1C from our manuscript (DOI pending)


SpliceV works with Python 2.7 and 3.0+.


  • Matplotlib
  • Numpy
  • pysam


To install SpliceV:

pip install SpliceV


git clone


To run the example dataset:

git clone 

cd SpliceV/example 

python ../bin/SpliceV -b example.vta1.bam -gtf vta1.gtf -sj example.canonical.bed -bsj example.circles.bed -g VTA1 -f 3 -is 3

The sample data comes from Akata cells (a B Cell Lymphoma line) that were treated with the exonuclease RNase R prior to sequencing. RNase R exclusively digests RNA with a free end, helping enrich circularized RNA abundance in the sample.

These example commands will generate the following plot: User example plot

This plot reveals a prominant circle from exon 2 through exon 4 (evidenced by the back-splice junction reads which are plotted as curves below the axis. This is also demonstrated by the higher level of coverage in exon 2-4, shown by the relative intensity of color).

User example plot explained

The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below:

User example circle


Created by Nathan Ungerleider and Erik Flemington

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