RSEM (RNA-Seq by Expectation-Maximization)


Jul 27, 2015   RSEM v1.2.22 is online now. Added options to run the STAR aligner.

May 6, 2015   RSEM v1.2.21 is online now. Strip read names of extra words to avoid mismatches of paired-end read names.

Mar 23, 2015   RSEM v1.2.20 is online now. Fixed a problem that can lead to assertion error if any paired-end read's insert size > 32767 (by changing the type of insertL in PairedEndHit.h from short to int).

Click here for full update information.


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


RSEM is under the GNU General Public License

Source Code



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 Jul 27, 2015)