This README describes the software SplAdder, short for Splicing Adder, a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data. The quantified events can then be used for differential analysis.
SplAdder relies on Python3 and requires only few standard packages that can be installed using a Python package manager of your choice (e.g., conda):
- scipy (version >= 0.12 tested)
- pysam (version >= 0.7 required)
- h5py (version >= 2.2.0 tested)
- intervaltree (version >= 3.0.1 tested)
- matplotlib (for the visualization code only; version >= 1.4.0 tested)
SplAdder will not run without these packages installed.
Previous versions of SplAdder were provided for both Matlab and Python. Since 2019, the Matlab code is no longer provided as part of the SplAdder package. If you are interested in the Matlab code, please download the initial release.
Please see the respective INSTALL files in the matlab or python directories for details on how to install SplAdder on your system.
Information on how to contact the authors can be found in the AUTHORS file.
All licensing information can be found in the COPYRIGHT file.
This README provides a quick walk-through of a basic SplAdder run. For further reading, please consider the SplAdder Wiki.
After installation, the command spladder becomes available in your path.
Invoking SplAdder without any parameters will print a description of the
command line interface to the screen.
In a basic call, SplAdder is invoked with three parameters: the annotation file (via -a), a comma separated list of alignment files (via -b) and an output directory where results files are stored (via -o). This will run SplAdder in its default configuration, which consists of the following steps:
- transform annotation into splicing graph representation
- generate an augmented splicing graph for each alignment file by inferring and
adding the following elements:
- insert intron retentions
- insert cassette exons
- insert new intron edges
- merge the augmented splicing graphs into a common splicing graph
- extract the following alternative splicing events:
- exon skip
- intron retention
- alternative 3'/5' splice site
- multiple exon skip
- mutually exclusive exons
- quantify all alternative splicing events on each of the provided alignment files