SplAdder 3.0.3-foss-2021b

Splicing Adder is 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.

Accessing SplAdder 3.0.3-foss-2021b

To load the module for SplAdder 3.0.3-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load SplAdder/3.0.3-foss-2021b

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the SplAdder website.

Dependencies

This version of SplAdder has a direct dependency on: foss/2021b h5py/3.6.0-foss-2021b matplotlib/3.4.3-foss-2021b numba/0.54.1-foss-2021b Pysam/0.18.0-GCC-11.2.0 Python/3.9.6-GCCcore-11.2.0 SciPy-bundle/2021.10-foss-2021b statsmodels/0.13.1-foss-2021b

Required By

This version of SplAdder is a direct dependent of: Bisbee/20210108-foss-2021b-R-4.2.0

Last modified on 7th October 2022