RSEM 2016

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RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation.

Installed version

The currently installed version is 1.3.1 on the environment hpc-env/6.4.

Using RSEM

If you want to find out more about RSEM on the HPC Cluster, you can use the command

module spider RSEM

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version, you must load the module as well as the environment:

module load hpc-env/6.4
module load RSEM

To get an overview of the available commands after loading RSEM, type in rsem- into your console and double tap the tabulator key. Now, the autocomplete function will show you every single command starting with rsem-, that is usable.


The full documentation about RSEM can be found in the Readme.

The developer's tutorial could be also helpful.

Further information are also available on the homepage