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RSEM specifications


Unique identifier OMICS_01287
Alternative names RNA-Seq by Expectation-Maximization, rsem
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl, Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.3.1
Stability Stable
Maintained Yes




No version available



  • person_outline Colin Dewey

Additional information

Publication for RNA-Seq by Expectation-Maximization

RSEM citations


Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross linking

Nat Commun
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w
call_split See protocol

[…] Normalized RSEM (abbreviation for RNA-Seq by Expectation Maximization) gene expression values of lung squamous cell carcinomas (n = 491 tumors) were obtained from TCGA, (data available on March 2014). Cohort exp […]


Circulating MiR 374a 5p is a potential modulator of the inflammatory process in obesity

Sci Rep
PMCID: 5955981
PMID: 29769661
DOI: 10.1038/s41598-018-26065-5

[…] t Kit, KAPA Biosystems).Read counts (expression levels) were obtained using a pipeline based on BowTie2 as alignment tool and the read count were determined using RNA-Seq by Expectation Maximization (RSEM).MicroRNAs with less than 10 counts in more than 90% of the samples were excluded. The data was normalized, using the weighted trimmed mean of M-values (TMM) method, an optimal method for the nor […]


Computational identification and validation of alternative splicing in ZSF1 rat RNA seq data, a preclinical model for type 2 diabetic nephropathy

Sci Rep
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] been developed to analyse alternative spliced transcripts in RNA-seq data. These tools can be divided into two categories based on their functionality. Tools in the first category include Cufflinks, RSEM, Kallisto, and Salmon, which can be applied to analyse known or annotated transcript isoforms. In this study, we chose Salmon, one of the top performers in speed and accuracy based on our interna […]


STT3 dependent PD L1 accumulation on cancer stem cells promotes immune evasion

Nat Commun
PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6
call_split See protocol

[…] The mRNA expression (RNA Seq V2 RSEM) database of TCGA Breast Invasive Carcinoma (n = 1100) was downloaded from the open-source resource of the cBioPortal for Cancer Genomics []. The log2 ratio of d […]


Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma

Nat Commun
PMCID: 5951856
PMID: 29760388
DOI: 10.1038/s41467-018-04008-y

[…] equenced to a target depth of 200-M reads on the Illumina HiSeq platform (Illumina, San Diego, CA). RNA samples were aligned to RefSeq build 73 transcriptome using Bowtie2 v2.2.6 and quantified using RSEM v1.2.25. […]


Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Nat Commun
PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] n analysis, we worked with read counts (as opposed to TPM), to be able to correct for sampling effects and allelic dropout.Gene expression measurements. Gene expression levels were measured using the RSEM software (version 1.2.16) RSEM was run on a merged FASTQ file for each sample, setting the ‘--bowtie2‘ flag and using Bowtie version 2.1.0, the ‘--num-threads‘ flag to 8, and ‘--calc-ci‘ flag. Th […]


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RSEM institution(s)
Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
RSEM funding source(s)
Supported partially by Dr. James Thomson’s MacArthur Professorship and by Morgridge Institute for Research support for Computation and Informatics in Biology and Medicine, and the NIH grant 1R01HG005232-01A1.

RSEM review

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Fabien Pichon

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Usefull if you want to estimate isoform expression in your RNA-seq. It uses Bowtie by default but you can map with another mapper and just use BAM/SAM file, so RSEM is quite flexible. Routinely used in TCGA workflow, but I would like to highlight that their RSEM UCSC isoforms IDs are sometimes different from Official UCSC isoforms IDs, no idea why...