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RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

RSEM is available as a module on Apocrita.


To run the default version of RSEM, simply load the rsem module:

$ module load rsem
Usage:   <command> [options] [--help]

The following commands are available:

convert-sam-for-rsem                         rsem-plot-model
extract-transcript-to-gene-map-from-trinity  rsem-plot-transcript-wiggles
rsem-bam2readdepth                           rsem-prepare-reference
rsem-bam2wig                                 rsem-preref
rsem-build-read-index                        rsem-refseq-extract-primary-assembly
rsem-calculate-credibility-intervals         rsem-run-em
rsem-calculate-expression                    rsem-run-gibbs
rsem-extract-reference-transcripts           rsem-sam-validator
rsem-generate-data-matrix                    rsem-scan-for-paired-end-reads
rsem-gen-transcript-plots                    rsem-simulate-reads
rsem-get-unique                              rsem-synthesis-reference-transcripts
rsem-gff3-to-gtf                             rsem-tbam2gbam

Usage for each command can be shown by using the command with the --help option. For more detailed documentation please check the link to the Github page listed below.

Core Usage

Not all RSEM commands support multi-threading; Commands which do support multi-threading should include a -p ${NSLOTS} or --num-threads ${NSLOTS} switch to use the correct number of cores. Please check the documentation before running jobs.

Example job

Serial job

Here is an example job running on 2 cores and 4GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load rsem

# Convert a transcript coordinate BAM alignments file into a genomic coordinate
BAM alignments file
rsem-tbam2gbam reference_name unsorted_transcript_bam_input genome_bam_output -p {NSLOTS}