Spladder
Description
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.
License
BSD Licence
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of spladder and load default version of spladder as
module avail spladder/ # list available modules module load spladder # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail spladder
and choose explicit version you want to use.
Documentation
https://github.com/ratschlab/spladder/wiki