Skip to main content

Visualize splice junctions, backsplice junctions (circleRNA) and coverage from RNA-Seq datasets

Project description

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

![Example plot](

## Documentation ##

## Example pipeline ##

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


git clone

## Example ##
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](

## Authors ##
Created by Nathan Ungerleider and Erik Flemington

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for SpliceV, version
Filename, size File type Python version Upload date Hashes
Filename, size SpliceV- (17.0 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size SpliceV- (16.0 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page