RSEM pipeline

RSEM specifications


Unique identifier OMICS_01287
Alternative names RNA-Seq by Expectation-Maximization, rsem
Software type Package/Module
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 1.3.0
Stability Stable
Requirements Bowtie
Maintained Yes



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  • person_outline Colin Dewey <>

Additional information

Publication for RNA-Seq by Expectation-Maximization

RSEM IN pipelines

PMCID: 5758489
PMID: 29313259
DOI: 10.1186/s13568-017-0529-4

[…] using a cut-off e-value of 10−5. to eliminate the influence of different gene lengths and sequence discrepancies on expression calculations, gene expression levels based on read counts obtained by rsem (version v1.2.15) were normalized using fpkm (fragments per kilo bases per million fragments) transformation (li and dewey 2011). the calculated gene expression levels were used for direct […]

PMCID: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] were performed by blastx with a cut-off e-value of 1e-5. unigenes having no homologs in the nr and swissprot databases were scanned using estscan [28]., gene expression levels were estimated by rsem [29]. for each sample, two biological replicates were sequenced and the correlation coefficients (r2) between replicates were calculated using pearson correlation. subsequently, the differential […]

PMCID: 5779695
PMID: 29360856
DOI: 10.1371/journal.pone.0191686

[…] terms ( of each c. medinalis unigene with the software blast2go ( using the default parameters [25]. gene expression level was normalized by rsem-based lgorithm to get rpkm value [26–27]. based on the expression levels, thresholds of fdr<0.05 and log2 fold-change (log2fc) ≥1 were set for identifying significant differential expressed […]

PMCID: 5786229
PMID: 29340581
DOI: 10.1093/gbe/evy001

[…] raw paired-end illumina reads (sra062458 and srp071466) were cleaned and trimmed using trimmomatic (bolger et al. 2014) and were used to estimate expression of αa and αd-globin in each species with rsem (li and dewey 2011). transcripts per million (tpm) was used as the expression metric., we integrated synteny, phylogenetic, and expression analyses to reconstruct the evolution of the α- […]

PMCID: 5789701
PMID: 29378643
DOI: 10.1186/s13059-017-1385-x

[…] pm and sequenced on a nextseq 500 (illumina)., rna-seq reads were aligned to the refseq hg38 transcriptome (grch38.2) using bowtie2 [49]. the resulting transcriptomic alignments were processed by rsem to estimate the abundance (expected counts and transcripts per million [tpm]) of refseq transcripts [50]., several genes were quantified multiple times due to alternative isoforms unrelated […]

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 in part by Dr. James Thomson’s MacArthur Professorship and by Morgridge Institute for Research support for Computation and Informatics in Biology and Medicine, and by 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...