spladder 2.2.2

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

What is SplAdder?

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.

Dependencies and Installation

SplAdder relies on Python3 and requires only few standard packages. A complete list of dependencies can be found in requirements.txt

We recommend using a python package manager such as anaconda to organize dependencies.

• Installation via pip: pip install spladder
• Installation from source:
  1. clone this repository
  2. Within the SplAdder root directory, run make install

Running Spladder

To start SplAdder and see a list of all available options, you can simply type:

spladder

Test with Example Data

If you installed SplAdder from source, you can test the installation by invoking make test in the SplAdder root directory.

Versions for Matlab and Python 2.7

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.

If you are interested in previous versions of SplAdder capable of running under Python 2.7, please use release 1.2.1. Please note, that the Python 2.7 code will be no longer maintained.

Authors

Information on how to contact the authors can be found in the AUTHORS file.

License and Disclaimer

All licensing information can be found in the COPYRIGHT file.

Documentation

This README provides only a high-level overview 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 in build-mode (spladder build), SplAdder requires at least 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