BEAR Applications

RNA-SeQC 1.1.8-foss-2019b-Java-11

There is a newer version of RNA-SeQC

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.

Accessing RNA-SeQC 1.1.8-foss-2019b-Java-11

To load the module for RNA-SeQC 1.1.8-foss-2019b-Java-11 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load RNA-SeQC/1.1.8-foss-2019b-Java-11

BEAR Apps Version

2019b

Architectures

EL8-cascadelake — EL8-haswell — 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 RNA-SeQC website.

Dependencies

This version of RNA-SeQC has a direct dependency on: BWA/0.7.17-GCC-8.3.0 foss/2019b Java/11

Required By

This version of RNA-SeQC is a direct dependent of: gtex-pipeline/gtex_v8-foss-2019b-Python-3.7.4-R-3.6.2

Other Versions

These versions of RNA-SeQC are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 17th June 2020