RSeQC
Description
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
License
GNU GPL 3
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 RSeQC and load default version of RSeQC as
module avail RSeQC/ # list available modules module load RSeQC # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail RSeQC
and choose explicit version you want to use.
After it you can type: python -c ‘from qcmodule import SAM’. If no error message comes out, RSeQC modules have been installed successfully.
Documentation
- Online documentation [1].
- Article about application and used algorithms RSeQC: quality control of RNA-seq experiments.