RSEM (RNA-Seq by Expectation-Maximization)


Nov 5, 2014   RSEM v1.2.19 is online now. Modified 'rsem-prepare-reference' such that by default it does not add any poly(A) tails. To add poly(A) tails, use '--polyA' option. Added an annotation of the 'sample_name.stat/sample_name.cnt' file, see 'cnt_file_description.txt'.

Sept 29, 2014   RSEM v1.2.18 is online now. Only generate warning message if two mates of a read pair have different names. Only parse attributes of a GTF record if its feature is "exon" to avoid unnecessary warning messages.

Sept 4, 2014   RSEM v1.2.17 is online now. Added error detection for cases such as a read's two mates having different names or a read is both alignable and unalignable.

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RSEM is mainly developed by Bo Li, who was a member of Deweylab.


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

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RSEM was developed with the help of Prof. Colin Dewey.

(last modified on Nov 5, 2014)