SpliceV

Visualize coverage, canonical, and backsplice junctions.

Documentation

See https://splicev.readthedocs.io/en/master/

Example pipeline

See https://github.com/flemingtonlab/SpliceV/blob/master/docs/example.pdf

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

Requirements

SpliceV works with Python 2.7 and 3.0+.

Dependencies

• Matplotlib
• Numpy
• pysam

Installation

To install SpliceV:

pip install SpliceV

Or:

git clone https://github.com/flemingtonlab/SpliceV.git

Example

To run the example dataset:

git clone https://github.com/flemingtonlab/SpliceV.git 

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:

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).

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

Authors

Created by Nathan Ungerleider and Erik Flemington