Skip to content
Visualize coverage, canonical, and backsplice junctions.
Python Shell
Branch: master
Clone or download
Latest commit 3d4a12d Aug 15, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
SpliceV fixed init Jan 3, 2019
bin made line split more backwards compatible Aug 15, 2019
build repackaged Aug 15, 2019
docs add example pdf Apr 26, 2019
etc added img Feb 21, 2019
example repackaged Aug 15, 2019
.gitattributes added gitattributes Jun 14, 2018
.gitignore png up Feb 20, 2019
LICENSE Create LICENSE Jun 14, 2018
MANIFEST.in fixed init Jan 3, 2019
README.md Update README.md Apr 26, 2019
setup.py repackaged Aug 15, 2019

README.md

SpliceV

Visualize coverage, canonical, and backsplice junctions.

Example plot

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: 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

Authors

Created by Nathan Ungerleider and Erik Flemington

You can’t perform that action at this time.