RSEM (RNA-Seq by Expectation-Maximization)


Mar 27, 2014   RSEM v1.2.12 is online now. Enabled allele-specific expression estimation. Added '--calc-pme' option for 'rsem-calculate-expression' to calculate posterior mean estimates only (no credibility intervals). Modified the shebang line of RSEM perl scripts to make them more portable. Added '--seed' option for 'rsem-simulate-reads' to enable users set the seed of random number generator used by the simulation. Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcripts that cannot be extracted, instead of failing the whole script, warning information is produced. Those transcripts are ignored.

Feb 14, 2014   RSEM v1.2.11 is online now. Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant alignments are not supported yet). Changed option names '--bowtie-phred33-quals', '--bowtie-phred64-quals' and '--bowtie-solexa-quals' back to '--phred33-quals', '--phred64-quals' and '--solexa-quals'.

Jan 31, 2014   RSEM v1.2.10 is online now. Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq.

Click here for full update information.


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

Simulation Data

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 Mar 27, 2014)