RNA-SeQC 2.4.2-foss-2021aRNA-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 2.4.2-foss-2021a
To load the module for RNA-SeQC 2.4.2-foss-2021a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load RNA-SeQC/2.4.2-foss-2021a
BEAR Apps Version
EL8-cascadelake — EL8-haswell — EL8-icelake
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.
- agutil 4.1.1
- pycryptodomex 3.9.8
- qtl 0.1.8
- rnaseqc 0.0.3
- rsa 4.6
For more information visit the RNA-SeQC website.
This version of RNA-SeQC has a direct dependency on: Boost/1.76.0-GCC-10.3.0 bx-python/0.8.11-foss-2021a bzip2/1.0.8-GCCcore-10.3.0 foss/2021a IPython/7.25.0-GCCcore-10.3.0 matplotlib/3.4.2-foss-2021a pyBigWig/0.3.18-foss-2021a Python/3.9.5-GCCcore-10.3.0 SciPy-bundle/2021.05-foss-2021a Seaborn/0.11.2-foss-2021a XZ/5.2.5-GCCcore-10.3.0 zlib/1.2.11-GCCcore-10.3.0
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.
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Last modified on 14th June 2022