Skip to content

RSEM

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

Conda installation

RSEM can be installed from the Bioconda Anaconda channel by loading the Miniforge module and then creating a Conda environment and installing RSEM into it (output below truncated):

$ module load miniforge
$ mamba create --quiet --yes --name rsem_env
$ mamba activate rsem_env
(rsem_env) $ mamba install bioconda::rsem

Looking for: ['bioconda::rsem']
...
  Updating specs:

   - bioconda::rsem
...
Confirm changes: [Y/n] Y
...
Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To take advantage of RSEM's built-in support for the Bowtie/Bowtie 2/HISAT2/STAR alignment program, you must install the relevant alignment package(s) in the same Conda environment as RSEM. The following command shows how to install all the listed alignment packages into the same environment as RSEM:

(rsem_env) $ mamba install -c bioconda bowtie2 hisat2 star

For compatibility, we recommend to not load any of these packages via modules.

Usage

To run RSEM, simply load the miniforge module and activate the Conda environment you installed it into:

module load miniforge
mamba activate rsem_env

After activating the Conda environment, 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
rsem-parse-alignments

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 official documentation before running jobs.

Example job

Serial job

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

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

module load miniforge
mamba activate rsem_env

# 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}

Reference