RSEM (RNA-Seq by Expectation-Maximization)


Feb 14, 2020   RSEM v1.3.3 is online now. Added HISAT2 option (--hisat2-hca) using Human Cell Atlas SMART-Seq2 pipeline parameters. Fixed a bug in RSEM simulator.

Apr 6, 2019   RSEM v1.3.2 is online now. Prevented RSEM from crashing when there is 0 aligned reads. Outputted theta and model files even there is no aligned reads.

Jun 27, 2018   RSEM v1.3.1 is online now. Added `--gff3-genes-as-transcripts` option for `rsem-prepare-reference`. This option will allow RSEM to treat genes as transcripts.

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Source Code



Bo Li and Colin Dewey designed the RSEM algorithm. Bo Li implemented the RSEM software. Peng Liu contributed the STAR aligner options and pRSEM.


RSEM is under the GNU General Public License

Prebuilt RSEM Indices (RSEM v1.1.17) for Galaxy Wrapper

These indices are based on RefSeq containing NM accession numbers only. That means only curated genes (no experimental, no miRNA, no noncoding). Only mature RNAs. In addition, 125bp Poly(A) tails are added at the end of each transcript.

Mouse Indices, extracted from mouse genome mm9

Human Indices, extracted from human genome hg18

Reference annotations and Simulation Data used in the paper

RefSeq and Ensembl annotation GTF files used in the paper

Simulation Data using Refseq set as reference

Simulation Data using Ensembl set as reference

Google Users and Announce Groups

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(last modified on Feb 14, 2020)